def test_configuration(self):
mol = make_water_fragment()
universe = M.universe('cube', [(mol, 'water', 10)])
# Missing data
self.assertRaises(TypeError,
lambda: M.Configuration(universe))
# Positions but no cell parameters
self.assertRaises(TypeError,
lambda: M.Configuration(universe,
IN.zeros((30, 3), N.float32)))
# Positions and cell parameters of different dtype
self.assertRaises(ValueError,
lambda: M.Configuration(universe,
IN.zeros((30, 3), N.float32),
N.float64(10.)))
# Positions not an array
self.assertRaises(TypeError,
lambda: M.Configuration(universe,
list(IN.zeros((30, 3),
N.float32)),
N.float32(10.)))
# Positions of wrong shape
self.assertRaises(ValueError,
lambda: M.Configuration(universe,
IN.zeros((25, 3), N.float32),
N.float32(10.)))
# Cell parameters of wrong shape
self.assertRaises(ValueError,
lambda: M.Configuration(universe,
IN.zeros((30, 3), N.float32),
IN.zeros((3,), N.float32)))
def test_parallelepiped(self):
universe = M.universe('parallelepiped', [(water, 'water', 100)])
nsites = universe.number_of_sites
conf1 = M.Configuration(universe,
IN.array(NR.normal(size=(nsites, 3))),
IN.array(NR.normal(size=(3, 3))))
conf2 = M.Configuration(universe,
IN.array(NR.normal(size=(nsites, 3))),
IN.array(NR.normal(size=(3, 3))))
self._write_and_read_back(universe, conf1, conf2)
def test_cubic(self):
universe = M.universe('cube', [(water, 'water', 10)])
nsites = universe.number_of_sites
conf1 = M.Configuration(universe,
IN.array(NR.normal(size=(nsites, 3))),
IN.array(10., N.float64))
conf2 = M.Configuration(universe,
IN.array(NR.normal(size=(nsites, 3))),
IN.array(11., N.float64))
self._write_and_read_back(universe, conf1, conf2)
def test_infinite(self):
universe = M.universe('infinite', [(water, 'water', 5)])
nsites = universe.number_of_sites
conf1 = M.Configuration(universe,
IN.array(NR.normal(size=(nsites, 3))),
None)
conf2 = M.Configuration(universe,
IN.array(NR.normal(size=(nsites, 3))),
None)
self._write_and_read_back(universe, conf1, conf2)
def _read_universe(self, el):
ref = el.get('ref', None)
if ref is not None:
return self._get_data(ref)
molecules = \
tuple(self._parse_molecule(el_m)
for el_m in el.iter('molecule'))
symmetry_transformations = \
tuple((self._array((3, 3), N.float64, el_t.find('rotation').text),
self._array((3,), N.float64, el_t.find('translation').text))
for el_t in el.iter('transformation'))
return im.universe(el.get('cell_shape'),
molecules,
symmetry_transformations,
el.get('convention'))
def test_universe(self):
mol = M.fragment("water", (),
(("H1", M.atom(M.element("H"), 8)),
("H2", M.atom(M.element("H"), 8)),
("O", M.atom(M.element("O"), 2))),
(("H1", "O", "single"), ("H2", "O", "single")))
self.assertRaises(TypeError,
lambda: M.universe(0, [(mol, 'water', 10)]))
self.assertRaises(ValueError,
lambda: M.universe('strange', [(mol, 'water', 10)]))
self.assertRaises(ValueError,
lambda: M.universe('strange', [(mol, 10)]))
self.assertRaises(TypeError,
lambda: M.universe('infinite', mol))
self.assertRaises(ValueError,
lambda: M.universe('infinite', [("water", 10)]))
self.assertRaises(TypeError,
lambda: M.universe('infinite', [mol]))
self.assertRaises(ValueError,
lambda: M.universe('infinite', [(10, mol)]))
self.assertRaises(ValueError,
lambda: M.universe('infinite', [(mol, 'water', 10)],
[(IN.zeros((3,3), N.float64),
IN.zeros((3,), N.float64))]))
def test_selection(self):
mol = make_water_fragment(nsites=2)
universe = M.universe('cube', [(mol, 'water', 5)])
# Index occurs twice
self.assertRaises(ValueError,
lambda: M.AtomSelection(universe,
IN.zeros((2,), N.uint16)))
# Atom index too large
self.assertRaises(ValueError,
lambda: M.AtomSelection(universe,
IN.array([20], N.uint16)))
# Template atom index too large
self.assertRaises(ValueError,
lambda: M.TemplateAtomSelection(universe,
IN.array([3], N.uint8)))
# Site index too large
self.assertRaises(ValueError,
lambda: M.SiteSelection(universe,
IN.array([40], N.uint16)))
# Template site index too large
self.assertRaises(ValueError,
lambda: M.TemplateSiteSelection(universe,
IN.array([8], N.uint8)))
def setUp(self):
self.infinite = M.universe('infinite', ())
self.cube = M.universe('cube', ())
self.cuboid = M.universe('cuboid', ())
self.parallelepiped = M.universe('parallelepiped', ())
def setUp(self):
mol = make_water_fragment(2)
self.universe = M.universe('infinite', [(mol, 'water', 10)],
convention='my_own')