def test_sidemax(self):
from mbuild.lib.molecules import Methane
ch4 = Methane()
#With default sidemax
box_of_methane = mb.fill_box(ch4,
box=[1000, 1000, 1000],
n_compounds=500)
sphere_of_methane = mb.fill_sphere(ch4,
sphere=[1000, 1000, 1000, 1000],
n_compounds=500)
assert all(box_of_methane.boundingbox.lengths < [110, 110, 110])
assert all(sphere_of_methane.boundingbox.lengths < [210, 210, 210])
#With adjusted sidemax
big_box_of_methane = mb.fill_box(ch4,
box=[1000, 1000, 1000],
n_compounds=500,
sidemax=1000.0)
big_sphere_of_methane = mb.fill_sphere(ch4,
sphere=[1000, 1000, 1000, 1000],
n_compounds=500,
sidemax=2000.0)
assert all(big_box_of_methane.boundingbox.lengths > [900, 900, 900])
assert all(
big_sphere_of_methane.boundingbox.lengths > [1800, 1800, 1800])
def test_validate_mass(self, methane):
bead = mb.Compound(name="A", mass=0.0)
with pytest.raises(MBuildError):
mb.fill_box(compound=bead, n_compounds=10, density=1)
with pytest.raises(MBuildError):
mb.fill_box(compound=bead, density=1, box=[0.5, 0.5, 0.5])
with pytest.raises(MBuildError):
mb.fill_sphere(compound=bead, sphere=[20, 20, 20, 20], density=1)
beadA = mb.Compound(name="A", mass=0.0)
beadB = mb.Compound(name="B", mass=1.0, pos=[0.5, 0.5, 0.5])
beads = mb.Compound(subcompounds=[beadA, beadB])
with warnings.catch_warnings(record=True) as w:
mb.packing._validate_mass(compound=[beadA, beadB],
n_compounds=None)
assert w
with warnings.catch_warnings(record=True) as w:
mb.packing._validate_mass(compound=[beads], n_compounds=None)
assert w
with warnings.catch_warnings(record=True) as w:
mb.packing._validate_mass(compound=[beads], n_compounds=[5])
assert w
def test_fill_sphere(self, h2o):
filled = mb.fill_sphere(h2o, sphere=[3, 3, 3, 1.5], n_compounds=50)
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
center = np.array([3.0, 3.0, 3.0])
assert np.alltrue(np.linalg.norm(filled.xyz - center, axis=1) < 1.5)
def test_fill_sphere(self, h2o):
filled = mb.fill_sphere(h2o, sphere=[3, 3, 3, 1.5], n_compounds=50)
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
center = np.array([3.0, 3.0, 3.0])
assert np.alltrue(np.linalg.norm(filled.xyz - center, axis=1) < 1.5)
def test_box_edge(self, h2o, methane):
system_box = mb.Box(lengths=(1.8, 1.8, 1.8))
packed = mb.fill_box(compound=h2o,
n_compounds=100,
box=system_box,
edge=0.2)
edge_sizes = system_box.lengths - packed.boundingbox.lengths
assert np.allclose(edge_sizes, np.array([0.4]*3), atol=0.1)
region = mb.fill_region(compound=h2o,
n_compounds=100,
region=system_box,
edge=0.2)
edge_sizes = system_box.lengths - packed.boundingbox.lengths
assert np.allclose(edge_sizes, np.array([0.4]*3), atol=0.1)
sphere = mb.fill_sphere(compound=h2o,
n_compounds=100,
sphere=[2, 2, 2, 1],
edge=0.2)
assert np.allclose(sphere.boundingbox.mins, np.array([1.2]*3), atol=0.1)
assert np.allclose(sphere.boundingbox.maxs, np.array([2.8]*3), atol=0.1)
solvated = mb.solvate(solvent=h2o,
solute=methane,
n_solvent=100,
box=system_box,
overlap=0.2)
edge_sizes = system_box.lengths - solvated.boundingbox.lengths
assert np.allclose(edge_sizes, np.array([0.4]*3), atol=0.1)
def test_fill_sphere_compound_ratio(self, h2o, ethane):
filled = mb.fill_sphere(compound=[h2o, ethane],
sphere=[3, 3, 3, 1.5],
density=800,
compound_ratio=[2, 1])
n_ethane = len([c for c in filled.children if c.name == 'Ethane'])
n_water = len([c for c in filled.children if c.name == 'H2O'])
assert n_water / n_ethane == 2
def test_box_edge(self, h2o, methane):
system_box = mb.Box(lengths=(1.8, 1.8, 1.8))
packed = mb.fill_box(compound=h2o,
n_compounds=100,
box=system_box,
edge=0.2)
edge_sizes = np.subtract(system_box.lengths,
packed.get_boundingbox().lengths)
assert np.allclose(edge_sizes, np.array([0.4] * 3), atol=0.1)
region = mb.fill_region(
compound=h2o,
n_compounds=100,
region=system_box,
edge=0.2,
bounds=[system_box],
)
edge_sizes = np.subtract(system_box.lengths,
packed.get_boundingbox().lengths)
assert np.allclose(edge_sizes, np.array([0.4] * 3), atol=0.1)
edge = 0.2
bounds = [2, 2, 2, 1]
sphere = mb.fill_sphere(compound=h2o,
n_compounds=100,
sphere=bounds,
edge=edge)
target_diameter = (bounds[3] - edge) * 2
assert np.allclose(sphere.maxs - sphere.mins,
np.array([target_diameter] * 3),
atol=0.1)
solvated = mb.solvate(
solvent=h2o,
solute=methane,
n_solvent=100,
box=system_box,
overlap=0.2,
)
edge_sizes = np.subtract(system_box.lengths,
solvated.get_boundingbox().lengths)
assert np.allclose(edge_sizes, np.array([0.4] * 3), atol=0.1)
def __init__(self, radius=2, angle=90.0, fluid=None, density=None,
lattice=None, lattice_compound=None, x=None, y=None):
super(GrapheneDroplet, self).__init__()
if fluid is None:
raise ValueError('Fluid droplet compounds must be specified')
if density is None:
raise ValueError('Fluid density must be specified (units kg/m^3)')
if x:
if x < radius * 4:
raise ValueError(
'Dimension x of sheet must be at least radius * 4')
elif x > 100:
raise ValueError(
'Dimension x of sheet must be less than 100 nm')
else:
x = radius * 4
if y:
if y < radius * 4:
raise ValueError(
'Dimension y of sheet must be at least radius * 4')
elif y > 100:
raise ValueError(
'Dimension y of sheet must be less than 100 nm')
else:
y = radius * 4
# Default to graphene lattice
if lattice is None:
if lattice_compound is not None:
raise ValueError(
'If Lattice is None, defaults to a Graphene surface. ' +
'In this case, do not specify lattice_compound.'
)
lattice_compound = mbuild.Compound(name='C')
lattice_spacing = [0.2456, 0.2456, 0.335]
angles = [90.0, 90.0, 120.0]
carbon_locations = [[0, 0, 0], [2 / 3, 1 / 3, 0]]
basis = {lattice_compound.name: carbon_locations}
lattice = mbuild.Lattice(
lattice_spacing=lattice_spacing,
angles=angles,
lattice_points=basis)
compound_dict = {lattice_compound.name: lattice_compound}
factor = np.cos(np.pi / 6) # fixes non-cubic lattice
# Estimate the number of lattice repeat units
replicate = [int(x / 0.2456), int(y / 0.2456) * (1 / factor)]
lat = lattice.populate(
compound_dict=compound_dict,
x=replicate[0],
y=replicate[1],
z=3
)
for particle in lat.particles():
if particle.xyz[0][0] < 0:
particle.xyz[0][0] += lat.periodicity[0]
lat.periodicity[1] *= factor
else:
if lattice_compound is None:
raise ValueError('Lattice compounds must be specified')
if not np.all(lattice.angles == 90.0):
raise ValueError(
'Currently, only cubic lattices are supported. ' +
'If using Graphene, do not pass in a Lattice.'
)
compound_dict = {lattice_compound.name: lattice_compound}
lat = lattice.populate(
compound_dict=compound_dict,
x=int(x/lattice.lattice_spacing[0]),
y=int(y/lattice.lattice_spacing[1]),
z=int(1.5/lattice.lattice_spacing[2]))
sheet = mbuild.clone(lat)
self.surface_height = np.max(sheet.xyz, axis=0)[2]
coords = list(sheet.periodicity)
height = get_height(radius, angle)
sphere_coords = [coords[0] / 2, coords[1] / 2, radius, radius]
sphere = mbuild.fill_sphere(
compound=fluid, sphere=sphere_coords, density=density)
to_remove = []
for child in sphere.children:
for atom_coords in child.xyz:
if height > radius:
if atom_coords[2] < height - radius:
to_remove += child
break
else:
if atom_coords[2] < height:
to_remove += child
break
sphere.remove(to_remove)
sheet.name = 'LAT'
sphere.name = 'FLD'
sphere.xyz -= [0, 0, np.min(sphere.xyz, axis=0)[2]]
sphere.xyz += [0, 0, self.surface_height + 0.3]
self.add(sheet)
self.add(sphere)
self.periodicity[0] = sheet.periodicity[0]
self.periodicity[1] = sheet.periodicity[1]
self.periodicity[2] = radius * 5
def test_fill_sphere_bad_args(self, h2o, ethane):
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o, sphere=[4, 4, 4, 1])
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o,
n_compounds=100,
density=100,
sphere=[4, 4, 4, 1])
with pytest.raises(TypeError):
mb.fill_sphere(compound=h2o, density=1000, sphere="yes")
with pytest.raises(ValueError):
mb.fill_sphere(compound=[h2o, ethane],
n_compounds=1000,
sphere=[1, 1, 1, 4])
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o,
n_compounds=[10, 10],
sphere=[1, 1, 1, 4])
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o, n_compounds=100, sphere=[1, 1, 1, 4])
def test_fill_sphere_density(self, h2o):
filled = mb.fill_sphere(h2o, sphere=[3, 3, 3, 1.5], density=1000)
assert filled.n_particles == 921
def test_fill_sphere_bad_args(self, h2o, ethane):
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o, sphere=[4, 4, 4, 1])
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o, n_compounds=100,
density=100, sphere=[4, 4, 4, 1])
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o, density=1000, sphere='yes')
with pytest.raises(ValueError):
mb.fill_sphere(compound=[h2o, ethane], n_compounds=1000, sphere=[1, 1, 1, 4])
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o, n_compounds=[10, 10], sphere=[1, 1, 1, 4])
with pytest.raises(ValueError):
mb.fill_sphere(compound=h2o, n_compounds=100, sphere=[1, 1, 1, 4])
def test_fill_sphere_compound_ratio(self, h2o, ethane):
filled = mb.fill_sphere(compound=[h2o, ethane], sphere=[3, 3, 3, 1.5],
density=800, compound_ratio=[2, 1])
n_ethane = len([c for c in filled.children if c.name == 'Ethane'])
n_water = len([c for c in filled.children if c.name == 'H2O'])
assert n_water / n_ethane == 2
def test_fill_sphere_density(self, h2o):
filled = mb.fill_sphere(h2o, sphere=[3, 3, 3, 1.5], density=1000)
assert filled.n_particles == 921
