class BackForthTests(unittest.TestCase):
def setUp(self):
self.cell = UnitCell(
Basis((2.5*angstrom,2.5*angstrom,10*angstrom,0,0,.5), kind = 'triclinic'),
(
(1./3,1./3,.5),
(2./3,2./3,.5),
),
'C',
)
coords = (numpy.linspace(0,1,11, endpoint = False),numpy.linspace(0,1,13, endpoint = False),numpy.linspace(0,1,17, endpoint = False))
self.grid = Grid(
self.cell,
coords,
numpy.zeros((11,13,17)),
)
self.grid.values = numpy.prod(numpy.sin(self.grid.explicit_coordinates()*2*numpy.pi), axis = -1)
def test_xsf_back_forth(self):
c1 = self.cell
cells = structure.xsf(xsf_structure(c1)).unitCells()
assert len(cells) == 1
c2 = cells[0]
assert c1.size() == c2.size()
testing.assert_allclose(c1.vectors/angstrom, c2.vectors/angstrom, atol = 1e-6)
testing.assert_allclose(c1.coordinates, c2.coordinates)
testing.assert_equal(c1.values, c2.values)
def test_xsf_back_forth_multi(self):
c1 = []
for i in range(10):
c = self.cell.copy()
c.coordinates += (numpy.random.rand(*c.coordinates.shape)-.5)/10
c1.append(c)
c2 = structure.xsf(xsf_structure(*c1)).unitCells()
for i,j in zip(c1,c2):
assert i.size() == j.size()
testing.assert_allclose(i.vectors/angstrom, j.vectors/angstrom, atol = 1e-6)
testing.assert_allclose(i.coordinates, j.coordinates)
testing.assert_equal(i.values, j.values)
def test_xsf_grid_back_forth(self):
data = xsf_grid(self.grid, self.cell)
g = structure.xsf(data).grids()[0]
testing.assert_allclose(self.grid.values, g.values, atol = 1e-7)
def test_qe_back_forth(self):
c1 = self.cell
c2 = qe.input(qe_input(
cell = c1,
pseudopotentials = {"C":"C.UPF"},
)).unitCell()
assert c1.size() == c2.size()
testing.assert_allclose(c1.vectors/angstrom, c2.vectors/angstrom, atol = 1e-6)
testing.assert_allclose(c1.coordinates, c2.coordinates)
testing.assert_equal(c1.values, c2.values)
def test_siesta_not_raises(self):
siesta_input(self.cell)
def test_openmx_back_forth(self):
c1 = self.cell
c2 = openmx.input(openmx_input(
c1,
populations = {"C": "2 2"},
)).unitCell()
assert c1.size() == c2.size()
testing.assert_allclose(c1.vectors/angstrom, c2.vectors/angstrom, atol = 1e-6)
testing.assert_allclose(c1.coordinates, c2.coordinates, rtol = 1e-6)
testing.assert_equal(c1.values, c2.values)
def test_openmx_back_forth_negf_0(self):
c1 = self.cell
c2 = openmx.input(openmx_input(
c1,
l = c1,
r = c1,
populations = {"C": "2 2"},
)).unitCell(l = c1, r = c1)
assert c1.size() == c2.size()
testing.assert_allclose(c1.vectors/angstrom, c2.vectors/angstrom, atol = 1e-6)
testing.assert_allclose(c1.coordinates, c2.coordinates, rtol = 1e-6)
testing.assert_equal(c1.values, c2.values)
def test_openmx_back_forth_negf_1(self):
c1 = self.cell.repeated(2,1,1)
l = self.cell
r = self.cell.repeated(3,1,1)
c2 = openmx.input(openmx_input(
c1,
l = l,
r = r,
populations = {"C": "2 2"},
)).unitCell(l = l, r = r)
assert c1.size() == c2.size()
testing.assert_allclose(c1.vectors/angstrom, c2.vectors/angstrom, atol = 1e-6)
testing.assert_allclose(c1.coordinates, c2.coordinates, rtol = 1e-6)
testing.assert_equal(c1.values, c2.values)
