def test_supercell():
from numpy import array, all, abs
from pylada.dftcrystal import Supercell, Crystal
from pylada.error import ValueError
structure = Crystal(136, 4.63909875, 2.97938395, \
ifhr=0, \
shift=0)\
.add_atom(0, 0, 0, 'Ti')\
.add_atom(0.306153, 0.306153, 0, 'O') \
.append(Supercell([[2,0,0],[0,1,0],[0,0,1]]))
assert len(structure.eval()) == 2 * 6
structure[-1].matrix[2,2] = 2
assert len(structure.eval()) == 2 * 2 * 6
map = structure[-1].output_map()
assert 'supercel' in map
a = Supercell()
a.read_input(map['supercel'])
assert all(abs(a.matrix - structure[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Supercell': Supercell}).matrix - a.matrix) < 1e-8)
# test errors
try: structure[-1].matrix = array( [[0]*3]*3 )
except ValueError: pass
else: raise Exception()
structure[-1].matrix = array([[1,0],[0,1]])
try: structure.print_input()
except ValueError: pass
else: raise Exception()
map = structure[-1].output_map()
assert 'supercel' in map
a = Supercell()
a.read_input(map['supercel'])
assert all(abs(a.matrix - structure[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Supercell': Supercell}).matrix - a.matrix) < 1e-8)
def test_crystal():
from numpy import array
from pylada.dftcrystal.crystal import Crystal
structure = Crystal(136, 4.63909875, 2.97938395, \
ifhr=0, \
shift=0)\
.add_atom(0, 0, 0, 'Ti')\
.add_atom(0.306153, 0.306153, 0, 'O')
assert structure.print_input() is not None
assert len(structure.print_input().split('\n')) == 9
assert all(abs(array(structure.print_input().split()[1:-2], dtype='float64') \
- [0, 0, 0, 136, 4.63909875, 2.97938395, 2, 22, 0, 0, 0, 8, 0.306153, 0.306153, 0]) < 1e-8)
assert structure.print_input().split()[0] == 'CRYSTAL'
assert structure.print_input().split()[-2] == 'END'
assert structure.print_input().split()[-1] == 'CRYSTAL'
def test_elastic():
""" Test elastic keyword. """
from pickle import loads, dumps
from numpy import array, all, abs, identity, dot
from pylada.dftcrystal import Crystal, Elastic
epsilon = array([[0, 0, 0], [0, 0, 0], [0, 0, 0.1]])
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
structure = crystal.eval()
crystal.append(Elastic([[0, 0, 0], [0, 0, 0], [0, 0, 0.1]]))
assert all(abs(dot(identity(3) + epsilon, structure.cell) - crystal.eval().cell) < 1e-8)
assert all(abs(crystal.eval()[0].pos - dot(identity(3) + epsilon, structure[0].pos)) < 1e-8)
assert all(abs(crystal.eval()[1].pos - dot(identity(3) + epsilon, structure[1].pos)) < 1e-8)
assert abs(crystal.eval()[0].pos[1] - crystal.eval()[0].pos[0]) < 1e-8
assert abs(crystal.eval()[1].pos[2] / crystal.eval()[1].pos[1] - 1.1) < 1e-8
assert abs(crystal.eval()[1].pos[1] - crystal.eval()[1].pos[0]) < 1e-8
a = Elastic()
a.raw = crystal[-1].raw
assert a.is_epsilon == crystal[-1].is_epsilon
assert all(abs(a.matrix - crystal[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Elastic': Elastic}).matrix - a.matrix) < 1e-8)
assert eval(repr(a), {'Elastic': Elastic}).is_epsilon == a.is_epsilon
assert loads(dumps(a)).is_epsilon == a.is_epsilon
assert all(abs(loads(dumps(a)).matrix - a.matrix) < 1e-8)
z = dot(epsilon, structure.cell)
crystal[-1].matrix = z
crystal[-1].is_epsilon = False
assert all(abs(dot(identity(3) + epsilon, structure.cell) - crystal.eval().cell) < 1e-8)
assert all(abs(crystal.eval()[0].pos - dot(identity(3) + epsilon, structure[0].pos)) < 1e-8)
assert all(abs(crystal.eval()[1].pos - dot(identity(3) + epsilon, structure[1].pos)) < 1e-8)
a = Elastic()
a.raw = crystal[-1].raw
assert a.is_epsilon == crystal[-1].is_epsilon
assert all(abs(a.matrix - crystal[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Elastic': Elastic}).matrix - a.matrix) < 1e-8)
assert eval(repr(a), {'Elastic': Elastic}).is_epsilon == a.is_epsilon
assert loads(dumps(a)).is_epsilon == a.is_epsilon
assert all(abs(loads(dumps(a)).matrix - a.matrix) < 1e-8)
epsilon = array([[0, 0, 0], [0, 0, 0], [0, 0.1, 0]])
crystal[-1].matrix = epsilon
crystal[-1].is_epsilon = True
assert all(abs(dot(identity(3) + epsilon, structure.cell) - crystal.eval().cell) < 1e-8)
assert all(abs(crystal.eval()[0].pos - dot(identity(3) + epsilon, structure[0].pos)) < 1e-8)
assert all(abs(crystal.eval()[1].pos - dot(identity(3) + epsilon, structure[1].pos)) < 1e-8)
a = Elastic()
a.raw = crystal[-1].raw
assert a.is_epsilon == crystal[-1].is_epsilon
assert all(abs(a.matrix - crystal[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Elastic': Elastic}).matrix - a.matrix) < 1e-8)
assert eval(repr(a), {'Elastic': Elastic}).is_epsilon == a.is_epsilon
assert loads(dumps(a)).is_epsilon == a.is_epsilon
assert all(abs(loads(dumps(a)).matrix - a.matrix) < 1e-8)
z = dot(epsilon, structure.cell)
crystal[-1].matrix = z
crystal[-1].is_epsilon = False
assert all(abs(dot(identity(3) + epsilon, structure.cell) - crystal.eval().cell) < 1e-8)
assert all(abs(crystal.eval()[0].pos - dot(identity(3) + epsilon, structure[0].pos)) < 1e-8)
assert all(abs(crystal.eval()[1].pos - dot(identity(3) + epsilon, structure[1].pos)) < 1e-8)
a = Elastic()
a.raw = crystal[-1].raw
assert a.is_epsilon == crystal[-1].is_epsilon
assert all(abs(a.matrix - crystal[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Elastic': Elastic}).matrix - a.matrix) < 1e-8)
assert eval(repr(a), {'Elastic': Elastic}).is_epsilon == a.is_epsilon
assert loads(dumps(a)).is_epsilon == a.is_epsilon
assert all(abs(loads(dumps(a)).matrix - a.matrix) < 1e-8)
def test_crystal():
from numpy import all, abs, array
from pylada.dftcrystal.crystal import Crystal
a = Crystal()
a.raw = '0 0 0\n'\
'136\n'\
'4.63909875 2.97938395\n'\
'2\n'\
'22 0.0 0.0 0.0\n'\
'8 3.061526467783E-01 3.061526467783E-01 0.0\n'
assert a.symmgroup == 136
assert a.shift == 0
assert a.ifhr == 0
assert len(a.atoms) == 2
assert a.atoms[0].type == 'Ti' and all(abs(a.atoms[0].pos) < 1e-8)
assert a.atoms[1].type == 'O' and all(abs(a.atoms[1].pos-[0.30615265, 0.30615265, 0.0]) < 1e-8)
a.raw = a.raw
assert a.symmgroup == 136
assert a.shift == 0
assert a.ifhr == 0
assert len(a.atoms) == 2
assert a.atoms[0].type == 'Ti' and all(abs(a.atoms[0].pos) < 1e-8)
assert a.atoms[1].type == 'O' and all(abs(a.atoms[1].pos-[0.30615265, 0.30615265, 0.0]) < 1e-8)
a.raw = '1 0 0\n'\
'P 42/M N M\n'\
'4.63909875 2.97938395\n'\
'2\n'\
'22 0.0 0.0 0.0\n'\
'8 3.061526467783E-01 3.061526467783E-01 0.0\n'
assert a.symmgroup == 'P 42/M N M'
a.raw = a.raw
assert a.symmgroup == 136
a.raw = '1 1 0\n'\
'P 42/M N M\n'\
'4.63909875 2.97938395\n'\
'2\n'\
'22 0.0 0.0 0.0\n'\
'8 3.061526467783E-01 3.061526467783E-01 0.0\n'
assert a.ifhr == 1
a.raw = a.raw
assert a.ifhr == 1
a.raw = '1 0 1\n'\
'P 42/M N M\n'\
'4.63909875 2.97938395\n'\
'2\n'\
'22 0.0 0.0 0.0\n'\
'8 3.061526467783E-01 3.061526467783E-01 0.0\n'
assert a.shift == 1
a.raw = a.raw
assert a.shift == 1
a.raw = '1 0 2\n'\
'P 42/M N M\n'\
'5 5 5\n'\
'4.63909875 2.97938395\n'\
'2\n'\
'22 0.0 0.0 0.0\n'\
'8 3.061526467783E-01 3.061526467783E-01 0.0\n'
assert all(abs(a.shift - 5/24.0) < 1e-8)
a.raw = a.raw
assert all(abs(a.shift - 5/24.0) < 1e-8)
b = eval(repr(a), {'Crystal': Crystal, 'array': array})
assert b.symmgroup == a.symmgroup
assert all(abs(array(b.params) - a.params) < 1e-8)
assert len(b) == len(a)
assert len(b.atoms) == len(a.atoms)
