def test_pass_box(self, mb_ethane):
mb_box = Box(lengths=[3, 3, 3])
top = from_mbuild(mb_ethane, box=mb_box)
assert_allclose_units(top.box.lengths, [3, 3, 3] * u.nm,
rtol=1e-5,
atol=1e-8)
def test_from_mbuild_single_particle(self):
compound = mb.Compound()
top = from_mbuild(compound)
assert top.n_sites == 1
assert top.n_subtops == 0
assert top.n_connections == 0
def test_full_conversion(self, ethane):
top = from_mbuild(ethane)
new = to_mbuild(top)
assert new.n_particles == 8
assert new.n_bonds == 7
def test_pass_box_bounding(self, mb_ethane):
mb_ethane.periodicity = [0, 0, 0]
top = from_mbuild(mb_ethane)
assert_allclose_units(
top.box.lengths,
(mb_ethane.boundingbox.lengths + [0.5, 0.5, 0.5]) * u.nm,
rtol=1e-5,
atol=1e-8)
def test_pass_box_bounding(self, mb_ethane):
mb_ethane.periodicity = [False, False, False]
top = from_mbuild(mb_ethane)
assert_allclose_units(
top.box.lengths,
(mb_ethane.get_boundingbox().lengths) * u.nm,
rtol=1e-5,
atol=1e-8,
)
def ar_system(self):
ar = mb.Compound(name='Ar')
packed_system = mb.fill_box(
compound=ar,
n_compounds=100,
box=mb.Box([3, 3, 3]),
)
return from_mbuild(packed_system)
def test_from_mbuild_ethane(self, ethane):
import mbuild as mb
top = from_mbuild(ethane)
assert top.n_sites == 8
assert top.n_subtops == 1
assert top.subtops[0].n_sites == 8
assert top.n_connections == 7
for i in range(top.n_sites):
assert isinstance(top.sites[i].element, gmso.Element)
assert top.sites[i].name == top.sites[i].element.symbol
def water_system(self):
water = mb.load(get_path('tip3p.mol2'))
water.name = 'water'
water[0].name = 'opls_111'
water[1].name = water[2].name = 'opls_112'
packed_system = mb.fill_box(compound=water,
n_compounds=2,
box=mb.Box([2, 2, 2]))
return from_mbuild(packed_system)
def test_3_layer_compound(self):
top_cmpnd = mb.Compound()
mid_cmpnd = mb.Compound()
bot_cmpnd = mb.Compound()
top_cmpnd.add(mid_cmpnd)
mid_cmpnd.add(bot_cmpnd)
top_cmpnd.periodicity = [1, 1, 1]
top = from_mbuild(top_cmpnd)
assert top.n_sites == 1
assert top.n_subtops == 1
assert top.subtops[0].n_sites == 1
def test_4_layer_compound(self):
l0_cmpnd = mb.Compound()
l1_cmpnd = mb.Compound()
l2_cmpnd = mb.Compound()
particle = mb.Compound()
l0_cmpnd.add(l1_cmpnd)
l1_cmpnd.add(l2_cmpnd)
l2_cmpnd.add(particle)
l0_cmpnd.periodicity = [1, 1, 1]
top = from_mbuild(l0_cmpnd)
assert top.n_sites == 1
assert top.n_subtops == 1
assert top.subtops[0].n_sites == 1
assert top.subtops[0].sites[0] == top.sites[0]
def test_uneven_hierarchy(self):
top_cmpnd = mb.Compound()
mid_cmpnd = mb.Compound()
particle1 = mb.Compound()
particle2 = mb.Compound()
top_cmpnd.add(mid_cmpnd)
top_cmpnd.add(particle1)
mid_cmpnd.add(particle2)
top_cmpnd.periodicity = [1, 1, 1]
top = from_mbuild(top_cmpnd)
assert top.n_sites == 2
assert top.n_subtops == 2
# Check that all sites belong to a subtop
site_counter = 0
for subtop in top.subtops:
site_counter += subtop.n_sites
assert site_counter == top.n_sites
def test_pass_box_periodicity(self, mb_ethane):
mb_ethane.periodicity = [2,2,2]
top = from_mbuild(mb_ethane)
assert_allclose_units(top.box.lengths, [2,2,2]*u.nm, rtol=1e-5, atol=1e-8)
def test_empty_compound_name(self):
compound = mb.load("CCOC", smiles=True)
top = from_mbuild(compound)
assert top.name is not None
def test_pass_box_bounding(self, ethane):
ethane.periodicity = [0, 0, 0]
top = from_mbuild(ethane)
assert allclose(top.box.lengths,
(ethane.boundingbox.lengths + [0.5, 0.5, 0.5]) * u.nm)
def test_pass_box_periodicity(self, ethane):
ethane.periodicity = [2, 2, 2]
top = from_mbuild(ethane)
assert allclose(top.box.lengths, [2, 2, 2] * u.nm)
def test_pass_failed_box(self, ethane):
with pytest.raises(ValueError):
top = from_mbuild(ethane, box=[3, 3, 3])
def test_pass_box(self, ethane):
mb_box = Box(lengths=[3, 3, 3])
top = from_mbuild(ethane, box=mb_box)
assert allclose(top.box.lengths, [3, 3, 3] * u.nm)
