#! /usr/bin/ruby1.9 -W require "helper" require 'stringio' class CrystalCell::Cell public :symmetry_operations end class FooCell < CrystalCell::Cell; end class TC_Cell < Test::Unit::TestCase $tolerance = 10 ** (-10) $symprec = 1.0e-05 $angle_tolerance = -1.0 def setup # 原子のないセル。 vectors00 = [[2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]] axes00 = CrystalCell::LatticeAxes.new([[2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]]) @c00 = CrystalCell::Cell.new(axes00) @c00.comment = 'c00' # 元素の識別子を数字にしたもの。 atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ), CrystalCell::Atom.new( 1, [0.1, 0.2, 0.3] ), ] @c01 = CrystalCell::Cell.new(axes00, atoms) @c01.comment = 'c01' # Li と O を1つずつ入れたセル。 # @c02 = CrystalCell::Cell.new( [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ] ) atoms = [ CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ), CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ), ] @c02 = CrystalCell::Cell.new(vectors00, atoms) @c02.comment = 'c02' # 原子の順序を逆にしたもの。 atoms = [ CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ), CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ), ] @c03 = CrystalCell::Cell.new(vectors00, atoms) @c03.comment = 'c03' # 原子の順序がいりまじったもの atoms = [ CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ), CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ), CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] ), ] @c04 = CrystalCell::Cell.new(vectors00, atoms) @c04.comment = 'c04' # 原子が不足しているもの。 atoms = [ CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ), ] @c05 = CrystalCell::Cell.new(vectors00, atoms) @c05.comment = 'c05' # Selective dynamics をいれたもの。 atoms = [ CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0], nil, [true, false, false ] ), CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ), ] @c06 = CrystalCell::Cell.new(vectors00, atoms) @c06.comment = 'c06' # 元素の識別子を数字にしたもの。 atoms = [ CrystalCell::Atom.new( 0, Mageo::Vector3DInternal[0.0, 0.0, 0.0] ), CrystalCell::Atom.new( 1, Mageo::Vector3DInternal[0.2, 0.2, 0.2] ), ] @c07 = CrystalCell::Cell.new(vectors00, atoms) @c07.comment = 'c07' # セル外の座標の原子を追加。 atoms = [ CrystalCell::Atom.new( 'Li', [ 1.2, 3.4, 5.6], "atom0", [ false, false, true] ), CrystalCell::Atom.new( 'O', [-1.2, -3.4, -5.6] ), ] @c08 = CrystalCell::Cell.new(vectors00, atoms) @c08.comment = 'c08' #cubic axes = CrystalCell::LatticeAxes.new( [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]] ) atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ) ] @c10 = CrystalCell::Cell.new( axes, atoms) @c10.comment = 'cubic' #hexagonal axes = CrystalCell::LatticeAxes.new( [ [0.86602540378443864676, 0.5, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0], ] ) atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ) ] @c11 = CrystalCell::Cell.new( axes, atoms) @c11.comment = 'hexagonal' #monoclinic axes = CrystalCell::LatticeAxes.new( [ [1.5, 1.4, 0.0], [0.0, 1.2, 0.0], [0.0, 0.0, 1.0], ] ) atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0]), #CrystalCell::Atom.new( 0, [0.1, 0.2, 0.3]), #CrystalCell::Atom.new( 0, [0.2, 0.3, 0.4]), ] @c12 = CrystalCell::Cell.new( axes, atoms) @c12.comment = 'monoclinic' #orthorhombic axes = CrystalCell::LatticeAxes.new( [ [3.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 1.0], ] ) atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0]) ] @c13 = CrystalCell::Cell.new( axes, atoms) @c13.comment = 'orthorhombic' #tetragonal axes = CrystalCell::LatticeAxes.new( [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 1.0], ] ) atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0], ) ] @c14 = CrystalCell::Cell.new( axes, atoms) @c14.comment = 'tetragonal' #tetragonal-b axes = CrystalCell::LatticeAxes.new( [ [2.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 2.0], ] ) atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0], ) ] @c14b = CrystalCell::Cell.new( axes, atoms) @c14b.comment = 'tetragonal-b' #triclinic axes = CrystalCell::LatticeAxes.new( [ [1.5, 1.4, 1.3], [0.0, 1.2, 1.1], [0.0, 0.0, 1.0], ] ) atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ), CrystalCell::Atom.new( 0, [0.1, 0.2, 0.3] ), CrystalCell::Atom.new( 0, [0.2, 0.3, 0.4] ), ] @c15 = CrystalCell::Cell.new( axes, atoms) @c15.comment = 'triclinic' #trigonal axes = CrystalCell::LatticeAxes.new( [ [0.86602540378443864676, 0.5, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0], ] ) atoms = [ CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0]), CrystalCell::Atom.new( 0, [0.333333333333333, 0.333333333333333, 0.333333333333333] ), ] @c16 = CrystalCell::Cell.new( axes, atoms) @c16.comment = 'trigonal' end def test_initialize la = CrystalCell::LatticeAxes.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ] ) c10 = CrystalCell::Cell.new( la ) c10.comment = 'c00' assert_equal( CrystalCell::Cell, c10.class ) assert_in_delta( 2.0, c10.axes[0][0], $tolerance ) assert_in_delta( 2.0, c10.axes[0][1], $tolerance ) assert_in_delta( 2.0, c10.axes[0][2], $tolerance ) assert_in_delta( 0.0, c10.axes[1][0], $tolerance ) assert_in_delta( 2.0, c10.axes[1][1], $tolerance ) assert_in_delta( 2.0, c10.axes[1][2], $tolerance ) assert_in_delta( 0.0, c10.axes[2][0], $tolerance ) assert_in_delta( 0.0, c10.axes[2][1], $tolerance ) assert_in_delta( 2.0, c10.axes[2][2], $tolerance ) end def test_positions assert_equal( [], @c00.positions) assert_equal( [ Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.2, 0.2, 0.2] ], @c02.positions ) assert_equal( [ Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.1, 0.2, 0.3] ], @c01.positions ) end def test_select_indices assert_equal( [], @c00.select_indices{ |i| i.element == "" } ) assert_equal( [], @c00.select_indices{ |i| i.element == "Li" } ) assert_equal( [] , @c01.select_indices{ |i| i.element == "" } ) assert_equal( [] , @c01.select_indices{ |i| i.element == "Li" } ) #@c01.select_indices{ |i| p i.element } assert_equal( [0], @c01.select_indices{ |i| i.element == 0 } ) assert_equal( [1], @c01.select_indices{ |i| i.element == 1 } ) assert_equal( [] , @c04.select_indices{ |i| i.element == "" } ) assert_equal( [0, 2], @c04.select_indices{ |i| i.element == "Li" } ) assert_equal( [1], @c04.select_indices{ |i| i.element == "O" } ) assert_equal( [ ], @c04.select_indices{ |i| i.element == 0 } ) assert_equal( [ ], @c04.select_indices{ |i| i.element == 1 } ) assert_equal( [1, 2], @c04.select_indices{ |i| i.position[0] > 0.05 } ) end def test_atoms_in_supercell t = @c02.atoms_in_supercell( 0, 0, 0, 0, 0, 1 ) assert_equal( 'Li', t[0].element ) assert_equal( 'Li', t[1].element ) assert_equal( 'O' , t[2].element ) assert_equal( 'O' , t[3].element ) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t[0].position ) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 1.0], t[1].position ) assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t[2].position ) assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 1.2], t[3].position ) t = @c02.atoms_in_supercell(-1, 1,-1, 1,-1, 1 ) assert_equal( ['Li']*27 + ['O'] * 27 , t.map{|i| i.element} ) assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, -1.0], t[ 0].position ) assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, 0.0], t[ 1].position ) assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, 1.0], t[ 2].position ) assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, -1.0], t[ 3].position ) assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, 0.0], t[ 4].position ) assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, 1.0], t[ 5].position ) assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, -1.0], t[ 6].position ) assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, 0.0], t[ 7].position ) assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, 1.0], t[ 8].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, -1.0], t[ 9].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, 0.0], t[10].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, 1.0], t[11].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, -1.0], t[12].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, 0.0], t[13].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, 1.0], t[14].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, -1.0], t[15].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, 0.0], t[16].position ) assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, 1.0], t[17].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, -1.0], t[18].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, 0.0], t[19].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, 1.0], t[20].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, -1.0], t[21].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, 0.0], t[22].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, 1.0], t[23].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, -1.0], t[24].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, 0.0], t[25].position ) assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, 1.0], t[26].position ) assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, -0.8], t[27].position ) assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, 0.2], t[28].position ) assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, 1.2], t[29].position ) assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, -0.8], t[30].position ) assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, 0.2], t[31].position ) assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, 1.2], t[32].position ) assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, -0.8], t[33].position ) assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, 0.2], t[34].position ) assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, 1.2], t[35].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, -0.8], t[36].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, 0.2], t[37].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, 1.2], t[38].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, -0.8], t[39].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 0.2], t[40].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 1.2], t[41].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, -0.8], t[42].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, 0.2], t[43].position ) assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, 1.2], t[44].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, -0.8], t[45].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, 0.2], t[46].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, 1.2], t[47].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, -0.8], t[48].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, 0.2], t[49].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, 1.2], t[50].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, -0.8], t[51].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, 0.2], t[52].position ) assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, 1.2], t[53].position ) end def test_elements assert_equal( [], @c00.elements) assert_equal( [ 'Li', 'O' ], @c02.elements ) assert_equal( [ 0, 1 ], @c01.elements ) end def test_add_atom assert_raise(ArgumentError){ @c00.add_atom('Li', [0.5, 0.5, 0.5] ) } @c00.add_atom(CrystalCell::Atom.new( 'Li', [0.5, 0.5, 0.5] )) assert_equal( 1 , @c00.atoms.size) assert_equal( 'Li' , @c00.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.5, 0.5, 0.5], @c00.atoms[0].position) assert_equal( nil , @c00.atoms[0].name ) @c00.add_atom(CrystalCell::Atom.new( nil , [0.5, 0.5, 0.5], 'A' )) assert_equal( 2 , @c00.atoms.size) assert_equal( nil , @c00.atoms[1].element) assert_equal( Mageo::Vector3DInternal[0.5, 0.5, 0.5], @c00.atoms[1].position) assert_equal( 'A' , @c00.atoms[1].name ) @c02.add_atom(CrystalCell::Atom.new( 'Li', [0.5, 0.5, 0.5] )) assert_equal( 3 , @c02.atoms.size) assert_equal( 'Li' , @c02.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c02.atoms[0].position) assert_equal( 'O' , @c02.atoms[1].element) assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], @c02.atoms[1].position) assert_equal( 'Li' , @c02.atoms[2].element) assert_equal( Mageo::Vector3DInternal[0.5, 0.5, 0.5], @c02.atoms[2].position) @c01.add_atom(CrystalCell::Atom.new( 'Li', [0.5, 0.5, 0.5] )) assert_equal( 3 , @c01.atoms.size) assert_equal( 0 , @c01.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c01.atoms[0].position) assert_equal( 1 , @c01.atoms[1].element) assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], @c01.atoms[1].position) assert_equal( 'Li' , @c01.atoms[2].element) assert_equal( Mageo::Vector3DInternal[0.5, 0.5, 0.5], @c01.atoms[2].position) end def test_delete_atom # assert_raise(RuntimeError ) {@c00.delete_atom( 0 ) } assert_equal(nil, @c00.delete_atom( 0 ) ) assert_equal([], @c00.positions ) assert_equal([], @c00.elements ) @c02.delete_atom( 0 ) assert_equal( [ Mageo::Vector3DInternal[0.2, 0.2, 0.2] ], @c02.positions) assert_equal( [ 'O' ], @c02.elements ) @c02.delete_atom( 0 ) assert_equal( [], @c02.positions) assert_equal( [], @c02.elements ) @c01.delete_atom( 0 ) assert_equal( [ Mageo::Vector3DInternal[0.1, 0.2, 0.3] ], @c01.positions) assert_equal( [ 1 ], @c01.elements ) end def test_set_elements # 原子がないので変更されない。 @c00.set_elements( [] ) assert_equal( [], @c00.atoms ) # 0 -> 'Li、 1 -> 'O' に変更。 tmp = Marshal.load( Marshal.dump( @c01 )) tmp.set_elements( [ 'Li', 'O' ] ) assert_equal( 'Li', tmp.atoms[0].element ) assert_equal( 'O', tmp.atoms[1].element ) # 0 -> 'Li, 片方だけ変更。 tmp = Marshal.load( Marshal.dump( @c01 )) tmp.set_elements( [ 'Li' ] ) assert_equal( 'Li', tmp.atoms[0].element ) assert_equal( 1, tmp.atoms[1].element ) # 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。 tmp = Marshal.load( Marshal.dump( @c02 )) tmp.set_elements( [ 'O', 'Li' ] ) assert_equal( 'Li', tmp.atoms[0].element ) assert_equal( 'O', tmp.atoms[1].element ) # Hash argument. # 0 -> 'Li、 1 -> 'O' に変更。 tmp = Marshal.load( Marshal.dump( @c01 )) tmp.set_elements( { 0 => 'Li', 1 => 'O' } ) assert_equal( 'Li', tmp.atoms[0].element ) assert_equal( 'O', tmp.atoms[1].element ) # 'Li' -> 'Na', 'O' -> 'S' に変更。 tmp = Marshal.load( Marshal.dump( @c02 )) tmp.set_elements( { 'Li' => 'Na', 'O' => 'S' } ) assert_equal( 'Na', tmp.atoms[0].element ) assert_equal( 'S', tmp.atoms[1].element ) # 'Li' -> 'Na'、 片方だけ変更。 tmp = Marshal.load( Marshal.dump( @c02 )) tmp.set_elements( { 'Li' => 'Na' } ) assert_equal( 'Na', tmp.atoms[0].element ) assert_equal( 'O', tmp.atoms[1].element ) end def test_equal_lattice_in_delta? assert_equal( true , @c00.equal_lattice_in_delta?(@c00, 0.001, 0.1) ) assert_equal( true , @c00.equal_lattice_in_delta?(@c02, 0.001, 0.1) ) assert_equal( true , @c00.equal_lattice_in_delta?(@c01, 0.001, 0.1) ) assert_equal( true , @c02.equal_lattice_in_delta?(@c00, 0.001, 0.1) ) assert_equal( true , @c02.equal_lattice_in_delta?(@c02, 0.001, 0.1) ) assert_equal( true , @c02.equal_lattice_in_delta?(@c01, 0.001, 0.1) ) assert_equal( true , @c01.equal_lattice_in_delta?(@c00, 0.001, 0.1) ) assert_equal( true , @c01.equal_lattice_in_delta?(@c02, 0.001, 0.1) ) assert_equal( true , @c01.equal_lattice_in_delta?(@c01, 0.001, 0.1) ) end def test_equal_atoms_in_delta? assert_equal( true , @c00.equal_atoms_in_delta?( @c00, 0.01 ) ) assert_equal( false, @c00.equal_atoms_in_delta?( @c02, 0.01 ) ) assert_equal( false, @c00.equal_atoms_in_delta?( @c01, 0.01 ) ) assert_equal( false, @c00.equal_atoms_in_delta?( @c03, 0.01 ) ) assert_equal( false, @c00.equal_atoms_in_delta?( @c04, 0.01 ) ) assert_equal( false, @c00.equal_atoms_in_delta?( @c05, 0.01 ) ) assert_equal( false, @c02.equal_atoms_in_delta?( @c00, 0.01 ) ) assert_equal( true , @c02.equal_atoms_in_delta?( @c02, 0.01 ) ) assert_equal( false, @c02.equal_atoms_in_delta?( @c01, 0.01 ) ) assert_equal( true , @c02.equal_atoms_in_delta?( @c03, 0.01 ) ) assert_equal( false, @c02.equal_atoms_in_delta?( @c04, 0.01 ) ) assert_equal( false, @c02.equal_atoms_in_delta?( @c05, 0.01 ) ) assert_equal( false, @c01.equal_atoms_in_delta?( @c00, 0.01 ) ) assert_equal( false, @c01.equal_atoms_in_delta?( @c02, 0.01 ) ) assert_equal( true , @c01.equal_atoms_in_delta?( @c01, 0.01 ) ) assert_equal( false, @c01.equal_atoms_in_delta?( @c03, 0.01 ) ) assert_equal( false, @c01.equal_atoms_in_delta?( @c04, 0.01 ) ) assert_equal( false, @c01.equal_atoms_in_delta?( @c05, 0.01 ) ) assert_equal( false, @c03.equal_atoms_in_delta?( @c00, 0.01 ) ) assert_equal( true , @c03.equal_atoms_in_delta?( @c02, 0.01 ) ) assert_equal( false, @c03.equal_atoms_in_delta?( @c01, 0.01 ) ) assert_equal( true , @c03.equal_atoms_in_delta?( @c03, 0.01 ) ) assert_equal( false, @c03.equal_atoms_in_delta?( @c04, 0.01 ) ) assert_equal( false, @c03.equal_atoms_in_delta?( @c05, 0.01 ) ) assert_equal( false, @c04.equal_atoms_in_delta?( @c00, 0.01 ) ) assert_equal( false, @c04.equal_atoms_in_delta?( @c02, 0.01 ) ) assert_equal( false, @c04.equal_atoms_in_delta?( @c01, 0.01 ) ) assert_equal( false, @c04.equal_atoms_in_delta?( @c03, 0.01 ) ) assert_equal( true , @c04.equal_atoms_in_delta?( @c04, 0.01 ) ) assert_equal( false, @c04.equal_atoms_in_delta?( @c05, 0.01 ) ) assert_equal( false, @c05.equal_atoms_in_delta?( @c00, 0.01 ) ) assert_equal( false, @c05.equal_atoms_in_delta?( @c02, 0.01 ) ) assert_equal( false, @c05.equal_atoms_in_delta?( @c01, 0.01 ) ) assert_equal( false, @c05.equal_atoms_in_delta?( @c03, 0.01 ) ) assert_equal( false, @c05.equal_atoms_in_delta?( @c04, 0.01 ) ) assert_equal( true , @c05.equal_atoms_in_delta?( @c05, 0.01 ) ) end def test_equal_in_delta? assert_equal(true , @c00.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c00.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c00.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c00.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c00.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c00.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c02.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c02.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) ) assert_equal(true , @c02.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) ) assert_equal(true , @c02.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c02.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c02.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c01.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) ) assert_equal(true , @c01.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c01.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c01.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c01.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c01.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c03.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c03.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) ) assert_equal(true , @c03.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) ) assert_equal(true , @c03.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c03.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c03.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c04.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c04.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c04.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c04.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) ) assert_equal(true , @c04.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c04.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c05.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c05.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c05.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c05.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) ) assert_equal(false, @c05.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) ) assert_equal(true , @c05.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) ) end def test_equal 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]])) assert_equal( true , @c00 == cell ) assert_equal( false, @c01 == cell ) 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]])) cell.add_atom(CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] )) cell.add_atom(CrystalCell::Atom.new( 1, [0.1, 0.2, 0.3] )) assert_equal( false, @c00 == cell ) assert_equal( true , @c01 == cell ) end def test_distance assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], [1,1,1])} assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], Mageo::Vector3DInternal[1,1,1])} assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], Mageo::Vector3D[1,1,1])} 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 ) assert_in_delta( Math::sqrt( 1.6**2 + 3.4**2 + 5.4**2), @c00.distance( Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.8, 0.9, 1.0] ), $tolerance ) 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 ) assert_in_delta( Math::sqrt( 1.6**2 + 3.4**2 + 5.4**2), @c00.distance( Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.8, 0.9, 1.0] ), $tolerance ) end def test_dump_poscar c00_str = [ 'c00', '1.0', ' 2.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 0.00000000000000 2.00000000000000', '', 'Direct' ].join("\n") c02_str = [ 'c02', '1.0', ' 2.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 0.00000000000000 2.00000000000000', ' 1 1', 'Direct', ' 0.00000000000000 0.00000000000000 0.00000000000000', ' 0.20000000000000 0.20000000000000 0.20000000000000' ].join("\n") c01_str = [ 'c01', '1.0', ' 2.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 0.00000000000000 2.00000000000000', ' 1 1', 'Direct', ' 0.00000000000000 0.00000000000000 0.00000000000000', ' 0.10000000000000 0.20000000000000 0.30000000000000' ].join("\n") c03_str = [ 'c03', '1.0', ' 2.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 0.00000000000000 2.00000000000000', ' 1 1', 'Direct', ' 0.00000000000000 0.00000000000000 0.00000000000000', ' 0.20000000000000 0.20000000000000 0.20000000000000' ].join("\n") c04_str = [ 'c04', '1.0', ' 2.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 0.00000000000000 2.00000000000000', ' 2 1', 'Direct', ' 0.00000000000000 0.00000000000000 0.00000000000000', ' 0.10000000000000 0.20000000000000 0.30000000000000', ' 0.20000000000000 0.20000000000000 0.20000000000000' ].join("\n") c05_str = [ 'c05', '1.0', ' 2.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 0.00000000000000 2.00000000000000', ' 1', 'Direct', ' 0.00000000000000 0.00000000000000 0.00000000000000' ].join("\n") c06_str = [ 'c06', '1.0', ' 2.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 2.00000000000000 2.00000000000000', ' 0.00000000000000 0.00000000000000 2.00000000000000', ' 1 1', 'Selective dynamics', 'Direct', ' 0.00000000000000 0.00000000000000 0.00000000000000 T F F', ' 0.20000000000000 0.20000000000000 0.20000000000000 T T T' ].join("\n") # Raise exception # assert_raise( RuntimeError ){ @c00.dump_poscar( [], io ) } assert_raise( RuntimeError ){ @c00.dump_poscar( [0] ) } assert_raise( RuntimeError ){ @c00.dump_poscar( [0, 1] ) } assert_raise( RuntimeError ){ @c00.dump_poscar( ['Li'] ) } assert_raise( RuntimeError ){ @c00.dump_poscar( ['Li', 'O'] ) } assert_raise( RuntimeError ){ @c02.dump_poscar( [] ) } assert_raise( RuntimeError ){ @c02.dump_poscar( [0] ) } assert_raise( RuntimeError ){ @c02.dump_poscar( [0, 1] ) } assert_raise( RuntimeError ){ @c02.dump_poscar( ['Li'] ) } assert_raise( RuntimeError ){ @c01.dump_poscar( [] ) } assert_raise( RuntimeError ){ @c01.dump_poscar( [0] ) } assert_raise( RuntimeError ){ @c01.dump_poscar( ['Li'] ) } assert_raise( RuntimeError ){ @c01.dump_poscar( ['Li', 'O'] ) } assert_raise( RuntimeError ){ @c04.dump_poscar( [] ) } assert_raise( RuntimeError ){ @c04.dump_poscar( [0] ) } assert_raise( RuntimeError ){ @c04.dump_poscar( [0, 1] ) } assert_raise( RuntimeError ){ @c04.dump_poscar( ['Li'] ) } assert_raise( RuntimeError ){ @c05.dump_poscar( [] ) } assert_raise( RuntimeError ){ @c05.dump_poscar( [0] ) } assert_raise( RuntimeError ){ @c05.dump_poscar( [0, 1] ) } assert_raise( RuntimeError ){ @c05.dump_poscar( ['Li', 'O'] ) } assert_raise( RuntimeError ){ @c03.dump_poscar( [] ) } assert_raise( RuntimeError ){ @c03.dump_poscar( [0] ) } assert_raise( RuntimeError ){ @c03.dump_poscar( [0, 1] ) } assert_raise( RuntimeError ){ @c03.dump_poscar( ['Li'] ) } # StringIO.new do |io| @c00.dump_poscar( [], io ) assert_equal( c00_str, io.read ) end StringIO.new do |io| @c02.dump_poscar( [ 'Li', 'O' ], io ) assert_equal( c02, io.read ) end StringIO.new do |io| @c01.dump_poscar( [ 0, 1 ], io ) assert_equal( c01, io.read ) end StringIO.new do |io| @c03.dump_poscar( [ 'Li', 'O' ], io ) assert_equal( c03, io.read ) end StringIO.new do |io| @c04.dump_poscar( [ 'Li', 'O' ], io ) assert_equal( c04, io.read ) end StringIO.new do |io| @c05.dump_poscar( [ 'Li', 'O' ], io ) assert_equal( c05, io.read ) end assert_equal( c00_str, @c00.dump_poscar( [ ], nil ) ) assert_equal( c01_str, @c01.dump_poscar( [ 0 , 1 ], nil ) ) assert_equal( c02_str, @c02.dump_poscar( [ 'Li', 'O' ], nil ) ) assert_equal( c03_str, @c03.dump_poscar( [ 'Li', 'O' ], nil ) ) assert_equal( c04_str, @c04.dump_poscar( [ 'Li', 'O' ], nil ) ) assert_equal( c05_str, @c05.dump_poscar( [ 'Li' ], nil ) ) assert_equal( c00_str, @c00.dump_poscar( [ ] ) ) assert_equal( c01_str, @c01.dump_poscar( [ 0 , 1 ] ) ) assert_equal( c02_str, @c02.dump_poscar( [ 'Li', 'O' ] ) ) assert_equal( c03_str, @c03.dump_poscar( [ 'Li', 'O' ] ) ) assert_equal( c04_str, @c04.dump_poscar( [ 'Li', 'O' ] ) ) assert_equal( c05_str, @c05.dump_poscar( [ 'Li' ] ) ) assert_equal( c06_str, @c06 .dump_poscar( [ 'Li', 'O' ] ) ) end def test_rotate @c02.add_atom(CrystalCell::Atom.new( 'Li', [1.1, 1.2, 1.3] )) assert_equal( [ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ], Mageo::Vector3DInternal[ -0.2, -0.2, -0.2 ], Mageo::Vector3DInternal[ -1.1, -1.2, -1.3 ] ], @c02.rotate( [[-1, 0, 0],[0, -1, 0],[0, 0, -1]] ).positions ) # Check not destructed. assert_equal( [ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ], Mageo::Vector3DInternal[ 0.2, 0.2, 0.2 ], Mageo::Vector3DInternal[ 1.1, 1.2, 1.3 ] ], @c02.positions ) end def test_rotate! @c02.add_atom(CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] )) @c02.rotate!( [[-1, 0, 0],[0, -1, 0],[0, 0, -1]] ) assert_equal( [ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ], Mageo::Vector3DInternal[ -0.2, -0.2, -0.2 ], Mageo::Vector3DInternal[ -0.1, -0.2, -0.3 ] ], @c02.positions ) end def test_translate poss = @c02.translate( [1.1, 1.2, 1.3] ).positions assert_in_delta( 1.1, poss[0][0], $tolerance ) assert_in_delta( 1.2, poss[0][1], $tolerance ) assert_in_delta( 1.3, poss[0][2], $tolerance ) assert_in_delta( 1.3, poss[1][0], $tolerance ) assert_in_delta( 1.4, poss[1][1], $tolerance ) assert_in_delta( 1.5, poss[1][2], $tolerance ) poss = @c02.translate( [-0.3,-0.3,-0.3] ).positions assert_in_delta( -0.3, poss[0][0], $tolerance ) assert_in_delta( -0.3, poss[0][1], $tolerance ) assert_in_delta( -0.3, poss[0][2], $tolerance ) assert_in_delta( -0.1, poss[1][0], $tolerance ) assert_in_delta( -0.1, poss[1][1], $tolerance ) assert_in_delta( -0.1, poss[1][2], $tolerance ) # Check not destructed. assert_equal( [ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ], Mageo::Vector3DInternal[ 0.2, 0.2, 0.2 ] ], @c02.positions ) end def test_translate! @c02.translate!( [1.1, 1.2, 1.3] ) poss = @c02.positions assert_in_delta( 1.1, poss[0][0], $tolerance ) assert_in_delta( 1.2, poss[0][1], $tolerance ) assert_in_delta( 1.3, poss[0][2], $tolerance ) assert_in_delta( 1.3, poss[1][0], $tolerance ) assert_in_delta( 1.4, poss[1][1], $tolerance ) assert_in_delta( 1.5, poss[1][2], $tolerance ) end def test_center_of_atoms # No atom in the cell. assert_raise( CrystalCell::Cell::NoAtomError ){ @c00.center_of_atoms } assert_equal( Mageo::Vector3DInternal[0.05, 0.1, 0.15], @c01.center_of_atoms ) assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c02.center_of_atoms ) assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c03.center_of_atoms ) assert_equal( Mageo::Vector3DInternal[0.1, 4.0/30.0, 5.0/30.0], @c04.center_of_atoms ) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c05.center_of_atoms ) assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c06.center_of_atoms ) assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c07.center_of_atoms ) end def test_calc_volume # @c00 = CrystalCell::Cell.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ] ) assert_in_delta( 8.00, @c00.calc_volume, $tolerance) c10 = CrystalCell::Cell.new( [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ] ) c11 = CrystalCell::Cell.new( [ [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5] ] ) assert_in_delta( 1.00, c10.calc_volume, $tolerance) assert_in_delta( 0.25, c11.calc_volume, $tolerance) end def test_cell_of_elements t = @c04.cell_of_elements( [ 'Li' ] ) assert_equal( CrystalCell::Cell, t.class ) assert_in_delta( 2.0, t.axes[0][0], $tolerance ) assert_in_delta( 2.0, t.axes[0][1], $tolerance ) assert_in_delta( 2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( 2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) # checking atom 1 assert_equal( 'Li' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) t = @c04.cell_of_elements( [ 'Li', 'O' ] ) assert_equal( CrystalCell::Cell, t.class ) assert_in_delta( 2.0, t.axes[0][0], $tolerance ) assert_in_delta( 2.0, t.axes[0][1], $tolerance ) assert_in_delta( 2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( 2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 3, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) # checking atom 2 assert_equal( 'Li' , t.atoms[2].element) assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[2].position) assert_equal( nil , t.atoms[2].name ) t = @c04.cell_of_elements( [ 'O' ] ) assert_equal( CrystalCell::Cell, t.class ) assert_in_delta( 2.0, t.axes[0][0], $tolerance ) assert_in_delta( 2.0, t.axes[0][1], $tolerance ) assert_in_delta( 2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( 2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 1, t.atoms.size ) # checking atom 0 assert_equal( 'O' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) t = @c04.cell_of_elements( [ 'F' ] ) assert_equal( CrystalCell::Cell, t.class ) assert_in_delta( 2.0, t.axes[0][0], $tolerance ) assert_in_delta( 2.0, t.axes[0][1], $tolerance ) assert_in_delta( 2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( 2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 0, t.atoms.size ) # サブクラスで使用したときに、サブクラスで作られるか？ fc04 = FooCell.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ] ) fc04.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] )) fc04.add_atom(CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] )) fc04.add_atom(CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] )) fc04.comment = 'fc04' t = fc04.cell_of_elements( [ 'Li' ] ) assert_equal( FooCell, t.class ) assert_in_delta( 2.0, t.axes[0][0], $tolerance ) assert_in_delta( 2.0, t.axes[0][1], $tolerance ) assert_in_delta( 2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( 2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) # checking atom 1 assert_equal( 'Li' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) end def test_unite ## 格子定数が違えば例外。将来的な feature. #t = CrystalCell::Cell.new( [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ] ) #t.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] )) #t.comment = 't' #assert_raise( CrystalCell::Cell::AxesMismatchError ){ @c05.unite( t ) } t = CrystalCell::Cell.new( [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ] ) t.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] )) t.comment = 't' assert_nothing_raised{ @c05.unite( t ) } # unite # 同じ座標のものがあっても気にせず統合する。 t = @c05.unite( @c06 ) assert_equal( CrystalCell::Cell, t.class ) assert_in_delta( 2.0, t.axes[0][0], $tolerance ) assert_in_delta( 2.0, t.axes[0][1], $tolerance ) assert_in_delta( 2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( 2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 3, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) # checking atom 1 assert_equal( 'Li' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) # checking atom 2 assert_equal( 'O' , t.atoms[2].element) assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[2].position) assert_equal( nil , t.atoms[2].name ) end def test_inverse_axis! @c02.inverse_axis!( 0 ) t = @c02 assert_equal( CrystalCell::Cell, t.class ) assert_in_delta(-2.0, t.axes[0][0], $tolerance ) assert_in_delta(-2.0, t.axes[0][1], $tolerance ) assert_in_delta(-2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( 2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) end def test_inverse_axis assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.inverse_axis( -1 ) } assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.inverse_axis( 3 ) } # x 軸反転 t = @c02.inverse_axis( 0 ) assert_equal( CrystalCell::Cell, t.class ) assert_in_delta( -2.0, t.axes[0][0], $tolerance ) assert_in_delta( -2.0, t.axes[0][1], $tolerance ) assert_in_delta( -2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( 2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) # checking non-destructive assert_equal( CrystalCell::Cell, t.class ) assert_in_delta( 2.0, @c02.axes[0][0], $tolerance ) assert_in_delta( 2.0, @c02.axes[0][1], $tolerance ) assert_in_delta( 2.0, @c02.axes[0][2], $tolerance ) assert_in_delta( 0.0, @c02.axes[1][0], $tolerance ) assert_in_delta( 2.0, @c02.axes[1][1], $tolerance ) assert_in_delta( 2.0, @c02.axes[1][2], $tolerance ) assert_in_delta( 0.0, @c02.axes[2][0], $tolerance ) assert_in_delta( 0.0, @c02.axes[2][1], $tolerance ) assert_in_delta( 2.0, @c02.axes[2][2], $tolerance ) assert_equal( 2, @c02.atoms.size ) # checking atom 0 assert_equal( 'Li' , @c02.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c02.atoms[0].position) assert_equal( nil , @c02.atoms[0].name ) # checking atom 1 assert_equal( 'O' , @c02.atoms[1].element) assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 0.2], @c02.atoms[1].position) assert_equal( nil , @c02.atoms[1].name ) # y 軸反転 # [ [ ax, ay, az], [ 0, by, bz], [ 0, 0, cz] ] # ↓ y 軸反転 # [ [ ax, ay, az], [ 0,-by,-bz], [ 0, 0, cz] ] # ↓ b vector の y 成分が正になるようにする。 # 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。 # [ [-ax,-ay, az], [ 0, by,-bz], [ 0, 0, cz] ] t = @c02.inverse_axis( 1 ) assert_equal( CrystalCell::Cell, t.class ) assert_in_delta( -2.0, t.axes[0][0], $tolerance ) assert_in_delta( -2.0, t.axes[0][1], $tolerance ) assert_in_delta( 2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta( -2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[ 0.2,-0.2, 0.2], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) # z 軸反転 # [ [ ax, ay, az], [ 0, by, bz], [ 0, 0, cz] ] # ↓ z 軸反転 # [ [ ax, ay, az], [ 0, by, bz], [ 0, 0,-cz] ] # ↓ c vector の z 成分が正になるようにする。 # b vector の y 成分も正であることを保存する回転は、 # y 軸回りに半回転し、全ての x, z 成分が反転する。 # [ [-ax, ay,-az], [ 0, by,-bz], [ 0, 0, cz] ] t = @c02.inverse_axis( 2 ) assert_equal( CrystalCell::Cell, t.class ) assert_in_delta(-2.0, t.axes[0][0], $tolerance ) assert_in_delta( 2.0, t.axes[0][1], $tolerance ) assert_in_delta(-2.0, t.axes[0][2], $tolerance ) assert_in_delta( 0.0, t.axes[1][0], $tolerance ) assert_in_delta( 2.0, t.axes[1][1], $tolerance ) assert_in_delta(-2.0, t.axes[1][2], $tolerance ) assert_in_delta( 0.0, t.axes[2][0], $tolerance ) assert_in_delta( 0.0, t.axes[2][1], $tolerance ) assert_in_delta( 2.0, t.axes[2][2], $tolerance ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position) assert_equal( nil , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2,-0.2], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) end def test_exchange_axes! # b, c の交換。 @c08.exchange_axes!( [ 1, 2 ] ) t = @c08 assert_equal( CrystalCell::Cell, t.class ) lc = t.axes.get_lattice_constants assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance ) assert_in_delta( 2.0 , lc[1], $tolerance ) assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[2], $tolerance ) assert_in_delta( 45.0000000000000, lc[3], $tolerance ) assert_in_delta( 35.2643896827547, lc[4], $tolerance ) assert_in_delta( 54.7356103172453, lc[5], $tolerance ) assert_equal( true, t.axes.lefthand? ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[ 1.2, 5.6, 3.4], t.atoms[0].position) assert_equal( 'atom0' , t.atoms[0].name ) assert_equal( [ false, false, true] , t.atoms[0].movable_flags ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[-1.2, -5.6, -3.4], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) end def test_exchange_axes assert_raise( CrystalCell::Cell::ArgumentError ){ @c02.exchange_axes( [ 0 ] ) } assert_raise( CrystalCell::Cell::ArgumentError ){ @c02.exchange_axes( [ 0, 1, 2] ) } assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.exchange_axes( [0, 3] ) } assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.exchange_axes( [-1, 2] ) } assert_raise( CrystalCell::Cell::SameAxesError ){ @c02.exchange_axes( [ 1,1] ) } # b, c の交換。 t = @c08.exchange_axes( [ 1, 2 ] ) assert_equal( CrystalCell::Cell, t.class ) lc = t.axes.get_lattice_constants assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance ) assert_in_delta( 2.0 , lc[1], $tolerance ) assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[2], $tolerance ) assert_in_delta( 45.0000000000000, lc[3], $tolerance ) assert_in_delta( 35.2643896827547, lc[4], $tolerance ) assert_in_delta( 54.7356103172453, lc[5], $tolerance ) assert_equal( true, t.axes.lefthand? ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[ 1.2, 5.6, 3.4], t.atoms[0].position) assert_equal( 'atom0' , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[-1.2, -5.6, -3.4], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) # b, c の交換によって非破壊であることを確認。 t = @c08 assert_equal( CrystalCell::Cell, t.class ) lc = t.axes.get_lattice_constants assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance ) assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance ) assert_in_delta( 2.0 , lc[2], $tolerance ) assert_in_delta( 45.0000000000000, lc[3], $tolerance ) assert_in_delta( 54.7356103172453, lc[4], $tolerance ) assert_in_delta( 35.2643896827547, lc[5], $tolerance ) assert_equal( true, t.axes.righthand? ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position) assert_equal( 'atom0' , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) end def test_reflect! @c08.reflect! t = @c08 assert_equal( CrystalCell::Cell, t.class ) lc = t.axes.get_lattice_constants assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance ) assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance ) assert_in_delta( 2.0 , lc[2], $tolerance ) assert_in_delta( 45.0000000000000, lc[3], $tolerance ) assert_in_delta( 54.7356103172453, lc[4], $tolerance ) assert_in_delta( 35.2643896827547, lc[5], $tolerance ) assert_equal( true, t.axes.lefthand? ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position) assert_equal( 'atom0' , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) end def test_reflect t = @c08.reflect assert_equal( CrystalCell::Cell, t.class ) lc = t.axes.get_lattice_constants assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance ) assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance ) assert_in_delta( 2.0 , lc[2], $tolerance ) assert_in_delta( 45.0000000000000, lc[3], $tolerance ) assert_in_delta( 54.7356103172453, lc[4], $tolerance ) assert_in_delta( 35.2643896827547, lc[5], $tolerance ) assert_equal( true, t.axes.lefthand? ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position) assert_equal( 'atom0' , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) # 非破壊であることを確認。 t = @c08 assert_equal( CrystalCell::Cell, t.class ) lc = t.axes.get_lattice_constants assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance ) assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance ) assert_in_delta( 2.0 , lc[2], $tolerance ) assert_in_delta( 45.0000000000000, lc[3], $tolerance ) assert_in_delta( 54.7356103172453, lc[4], $tolerance ) assert_in_delta( 35.2643896827547, lc[5], $tolerance ) assert_equal( true, t.axes.righthand? ) assert_equal( 2, t.atoms.size ) # checking atom 0 assert_equal( 'Li' , t.atoms[0].element) assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position) assert_equal( 'atom0' , t.atoms[0].name ) # checking atom 1 assert_equal( 'O' , t.atoms[1].element) assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position) assert_equal( nil , t.atoms[1].name ) end def test_operate # identity operation rotation = [ [1, 0, 0], [0, 1, 0], [0, 0, 1], ] translation = [0.0, 0.0, 0.0] result = @c01.operate(rotation, translation) assert_in_delta( 0.0, result.atoms[0].position[0], $tolerance) assert_in_delta( 0.0, result.atoms[0].position[1], $tolerance) assert_in_delta( 0.0, result.atoms[0].position[2], $tolerance) assert_in_delta( 0.1, result.atoms[1].position[0], $tolerance) assert_in_delta( 0.2, result.atoms[1].position[1], $tolerance) assert_in_delta( 0.3, result.atoms[1].position[2], $tolerance) # rotation rotation = [ [1, 0, 0], [0, 1, 0], [0, 0,-1], ] translation = [0.0, 0.0, 0.0] result = @c01.operate(rotation, translation) assert_in_delta( 0.0, result.atoms[0].position[0], $tolerance) assert_in_delta( 0.0, result.atoms[0].position[1], $tolerance) assert_in_delta( 0.0, result.atoms[0].position[2], $tolerance) assert_in_delta( 0.1, result.atoms[1].position[0], $tolerance) assert_in_delta( 0.2, result.atoms[1].position[1], $tolerance) assert_in_delta(-0.3, result.atoms[1].position[2], $tolerance) # translation rotation = [ [1, 0, 0], [0, 1, 0], [0, 0, 1], ] translation = [0.1, 0.2, 0.3] result = @c01.operate(rotation, translation) assert_in_delta(0.1, result.atoms[0].position[0], $tolerance) assert_in_delta(0.2, result.atoms[0].position[1], $tolerance) assert_in_delta(0.3, result.atoms[0].position[2], $tolerance) assert_in_delta(0.2, result.atoms[1].position[0], $tolerance) assert_in_delta(0.4, result.atoms[1].position[1], $tolerance) assert_in_delta(0.6, result.atoms[1].position[2], $tolerance) # rotation & translation rotation = [ [1, 0, 0], [0, 1, 0], [0, 0,-1], ] translation = [0.1, 0.2, 0.3] result = @c01.operate(rotation, translation) assert_in_delta(0.1, result.atoms[0].position[0], $tolerance) assert_in_delta(0.2, result.atoms[0].position[1], $tolerance) assert_in_delta(0.3, result.atoms[0].position[2], $tolerance) assert_in_delta(0.2, result.atoms[1].position[0], $tolerance) assert_in_delta(0.4, result.atoms[1].position[1], $tolerance) assert_in_delta(0.0, result.atoms[1].position[2], $tolerance) end def test_axis_independencies unless defined? Getspg puts puts "test_axis_independencies() is ignored because spglib is not installed." return end assert_equal([false, false, false], @c10 .axis_independencies($symprec, $angle_tolerance)) assert_equal([false, false, true ], @c11 .axis_independencies($symprec, $angle_tolerance)) assert_equal([true , true , true ], @c12 .axis_independencies($symprec, $angle_tolerance)) assert_equal([true , true , true ], @c13 .axis_independencies($symprec, $angle_tolerance)) assert_equal([false, false, true ], @c14 .axis_independencies($symprec, $angle_tolerance)) assert_equal([false, true , false], @c14b.axis_independencies($symprec, $angle_tolerance)) assert_equal([true , true , true ], @c15 .axis_independencies($symprec, $angle_tolerance)) assert_equal([false, false, true ], @c16 .axis_independencies($symprec, $angle_tolerance)) end def test_symmetry_operations unless defined? Getspg puts puts "test_symmetry_operations() is ignored because spglib is not installed." return end f13 = 1.0/3.0 #cubic/POSCAR #Pm-3m (221) / m-3m / -P 4 2 3 (517) corrects = [ {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02---- {:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03---- {:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----05---- {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----06---- {:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----07---- {:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----08---- {:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----09---- {:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----10---- {:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----11---- {:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----12---- {:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13---- {:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14---- {:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----15---- {:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----16---- {:rotation => [[ 0, 0, 1], [ 1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----17---- {:rotation => [[ 0, 0, -1], [-1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----18---- {:rotation => [[ 0, 0, 1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----19---- {:rotation => [[ 0, 0, -1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----20---- {:rotation => [[ 0, 0, 1], [-1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----21---- {:rotation => [[ 0, 0, -1], [ 1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----22---- {:rotation => [[ 0, 0, 1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----23---- {:rotation => [[ 0, 0, -1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----24---- {:rotation => [[ 0, 0, -1], [ 1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----25---- {:rotation => [[ 0, 0, 1], [-1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----26---- {:rotation => [[ 0, 0, -1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----27---- {:rotation => [[ 0, 0, 1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----28---- {:rotation => [[ 0, 0, -1], [-1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----29---- {:rotation => [[ 0, 0, 1], [ 1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----30---- {:rotation => [[ 0, 0, -1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----31---- {:rotation => [[ 0, 0, 1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----32---- {:rotation => [[ 0, 1, 0], [ 0, 0, 1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----33---- {:rotation => [[ 0, -1, 0], [ 0, 0, -1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----34---- {:rotation => [[ 1, 0, 0], [ 0, 0, 1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----35---- {:rotation => [[-1, 0, 0], [ 0, 0, -1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----36---- {:rotation => [[ 0, -1, 0], [ 0, 0, 1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----37---- {:rotation => [[ 0, 1, 0], [ 0, 0, -1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----38---- {:rotation => [[-1, 0, 0], [ 0, 0, 1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----39---- {:rotation => [[ 1, 0, 0], [ 0, 0, -1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----40---- {:rotation => [[ 0, -1, 0], [ 0, 0, -1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----41---- {:rotation => [[ 0, 1, 0], [ 0, 0, 1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----42---- {:rotation => [[-1, 0, 0], [ 0, 0, -1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----43---- {:rotation => [[ 1, 0, 0], [ 0, 0, 1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----44---- {:rotation => [[ 0, 1, 0], [ 0, 0, -1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----45---- {:rotation => [[ 0, -1, 0], [ 0, 0, 1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----46---- {:rotation => [[ 1, 0, 0], [ 0, 0, -1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----47---- {:rotation => [[-1, 0, 0], [ 0, 0, 1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----48---- ] results = @c10 .symmetry_operations($symprec, $angle_tolerance) assert_equal(corrects.size, results.size) corrects.size.times do |index| assert_equal(corrects[index], results[index]) end #hexagonal/POSCAR #P6/mmm (191) / 6/mmm/ -P 6 2 (485) corrects = [ {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02---- {:rotation => [[ 0, -1, 0], [ 1, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03---- {:rotation => [[ 0, 1, 0], [-1, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04---- {:rotation => [[-1, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----05---- {:rotation => [[ 1, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----06---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----07---- {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----08---- {:rotation => [[ 0, 1, 0], [-1, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----09---- {:rotation => [[ 0, -1, 0], [ 1, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----10---- {:rotation => [[ 1, 1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----11---- {:rotation => [[-1, -1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----12---- {:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13---- {:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14---- {:rotation => [[ 1, 1, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----15---- {:rotation => [[-1, -1, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----16---- {:rotation => [[ 1, 0, 0], [-1, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----17---- {:rotation => [[-1, 0, 0], [ 1, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----18---- {:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----19---- {:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----20---- {:rotation => [[-1, -1, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----21---- {:rotation => [[ 1, 1, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----22---- {:rotation => [[-1, 0, 0], [ 1, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----23---- {:rotation => [[ 1, 0, 0], [-1, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----24---- ] assert_equal(corrects, @c11 .symmetry_operations($symprec, $angle_tolerance)) #hexagonal #monoclinic/POSCAR #P2/m (10) / 2/m / -P 2y (57) corrects = [ {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03---- {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04---- ] #pp @c12 assert_equal(corrects, @c12 .symmetry_operations($symprec, $angle_tolerance)) #monoclinic #orthorhombic/POSCAR #Pmmm (47) / mmm / -P 2 2 (227) corrects = [ {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03---- {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04---- {:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----05---- {:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----06---- {:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----07---- {:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----08---- ] assert_equal(corrects, @c13 .symmetry_operations($symprec, $angle_tolerance)) #orthorhombic #tetragonal-b/POSCAR #P4/mmm (123) / 4/mmm/ -P 4 2 (400) corrects = [ {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02---- {:rotation => [[ 0, 0, 1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----03---- {:rotation => [[ 0, 0, -1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----04---- {:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----05---- {:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----06---- {:rotation => [[ 0, 0, -1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----07---- {:rotation => [[ 0, 0, 1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----08---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----09---- {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----10---- {:rotation => [[ 0, 0, -1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----11---- {:rotation => [[ 0, 0, 1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----12---- {:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13---- {:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14---- {:rotation => [[ 0, 0, 1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----15---- {:rotation => [[ 0, 0, -1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----16---- ] assert_equal(corrects, @c14b .symmetry_operations($symprec, $angle_tolerance)) #tetragonal #tetragonal/POSCAR #P4/mmm (123) / 4/mmm/ -P 4 2 (400) corrects = [ {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02---- {:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03---- {:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----05---- {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----06---- {:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----07---- {:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----08---- {:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----09---- {:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----10---- {:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----11---- {:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----12---- {:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13---- {:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14---- {:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----15---- {:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----16---- ] assert_equal(corrects, @c14.symmetry_operations($symprec, $angle_tolerance)) #tetragonal-b #triclinic/POSCAR #P1 (1) / 1 / P 1 (1) corrects = [ {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01---- ] assert_equal(corrects, @c15 .symmetry_operations($symprec, $angle_tolerance)) #triclinic #trigonal/POSCAR #P-3m1 (164) / -3m / -P 3 2= (456) corrects = [ {:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01---- {:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----02---- {:rotation => [[-1, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----03---- {:rotation => [[ 1, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----04---- {:rotation => [[ 0, 1, 0], [-1, -1, 0], [ 0, 0, 1]], :translation => [1.0, 0.0, 1.0]}, #----05---- {:rotation => [[ 0, -1, 0], [ 1, 1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----06---- {:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----07---- {:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [1.0, 0.0, 1.0]}, #----08---- {:rotation => [[-1, 0, 0], [ 1, 1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----09---- {:rotation => [[ 1, 0, 0], [-1, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----10---- {:rotation => [[ 1, 1, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----11---- {:rotation => [[-1, -1, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----12---- ] results = @c16.symmetry_operations($symprec, $angle_tolerance) corrects.size.times do |index| 3.times do |i| 3.times do |j| assert_in_delta( corrects[index][:rotation][i][j], results[index][:rotation][i][j], $tolerance ) end end 3.times do |i| assert_in_delta( corrects[index][:translation][i], results[index][:translation][i], $tolerance ) end end end end