def test_bad_args(self, h2o):
with pytest.raises(ValueError):
mb.fill_box(h2o, n_compounds=10)
with pytest.raises(ValueError):
mb.fill_box(h2o, density=1000)
with pytest.raises(ValueError):
mb.fill_box(h2o, box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_box(h2o, n_compounds=10, density=1000, box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_box(compound=[h2o, h2o], n_compounds=[10], density=1000)
with pytest.raises(ValueError):
mb.solvate(solute=h2o,
solvent=[h2o],
n_solvent=[10, 10],
box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_region(h2o,
n_compounds=[10, 10],
region=[2, 2, 2, 4, 4, 4])
with pytest.raises(ValueError):
mb.fill_box(
compound=[h2o, h2o],
n_compounds=[10],
density=1000,
fix_orientation=[True, True, True],
)
def __init__(self,
pore_depth=4,
side_dim=3,
n_sheets=3,
pore_width=1,
x_bulk=3,
solvent=None,
n_solvent=100):
super(GraphenePoreSolvent, self).__init__()
pore = GraphenePore(pore_depth=pore_depth,
side_dim=side_dim,
n_sheets=n_sheets,
pore_width=pore_width)
box = mb.Box(pore.periodicity)
box.maxs[0] += 2 * x_bulk
system = mb.solvate(pore, solvent, n_solvent, box=box, overlap=0.2)
for child in system.children:
self.add(mb.clone(child))
self.periodicity = box.maxs
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_write_temp_file(self, h2o):
cwd = os.getcwd() # Must keep track of the temp dir that pytest creates
filled = mb.fill_box(h2o, n_compounds=10, box=[4, 4, 4], temp_file='temp_file1.pdb')
region = mb.fill_region(h2o, 10, [2, 2, 2, 4, 4, 4], temp_file='temp_file2.pdb')
solvated = mb.solvate(filled, h2o, 10, box=[4, 4, 4], temp_file='temp_file3.pdb')
assert os.path.isfile(os.path.join(cwd, 'temp_file1.pdb'))
assert os.path.isfile(os.path.join(cwd, 'temp_file2.pdb'))
assert os.path.isfile(os.path.join(cwd, 'temp_file3.pdb'))
def test_write_temp_file(self, h2o):
cwd = os.getcwd() # Must keep track of the temp dir that pytest creates
filled = mb.fill_box(h2o, n_compounds=10, box=[4, 4, 4], temp_file='temp_file1.pdb')
region = mb.fill_region(h2o, 10, [2, 2, 2, 4, 4, 4], temp_file='temp_file2.pdb')
solvated = mb.solvate(filled, h2o, 10, box=[4, 4, 4], temp_file='temp_file3.pdb')
assert os.path.isfile(os.path.join(cwd, 'temp_file1.pdb'))
assert os.path.isfile(os.path.join(cwd, 'temp_file2.pdb'))
assert os.path.isfile(os.path.join(cwd, 'temp_file3.pdb'))
def test_bad_args(self, h2o):
with pytest.raises(ValueError):
mb.fill_box(h2o, n_compounds=10)
with pytest.raises(ValueError):
mb.fill_box(h2o, density=1000)
with pytest.raises(ValueError):
mb.fill_box(h2o, box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_box(h2o, n_compounds=10, density=1000, box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_box(compound=[h2o, h2o], n_compounds=[10], density=1000)
with pytest.raises(ValueError):
mb.solvate(solute=h2o, solvent=[h2o], n_solvent=[10, 10], box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_region(h2o, n_compounds=[10, 10], region=[2, 2, 2, 4, 4, 4])
with pytest.raises(ValueError):
mb.fill_box(compound=[h2o, h2o], n_compounds=[10], density=1000,
fix_orientation=[True, True, True])
def __init__(self,
solv,
n_solvent,
length=3,
radius=None,
chirality="armchair",
n=None,
m=None,
superPacked=False):
super(SWCNT_solvated, self).__init__(length,
radius=radius,
chirality=chirality,
n=n,
m=m)
#Quick method packs molecules into smaller box but with a higher density
if superPacked:
minimums = (self.r * np.cos(.75 * np.pi),
self.r * np.cos(.25 * np.pi), 0)
maximums = (self.r * np.cos(.25 * np.pi),
self.r * np.cos(.75 * np.pi), length)
box = mb.Box(mins=minimums, maxs=maximums)
mb.solvate(self, solv, n_solvent, box=box)
#Slow method carves out cyilnder of molecules from box of proper
#density molecules silghtly larger than the nanotube
else:
s = mb.Compound(name="Temp")
box = mb.Box(mins=(-self.r, -self.r, 0),
maxs=(self.r, self.r, length))
print(box)
s = mb.solvate(s, solv, n_solvent, box)
for child in s:
if child.pos[0] < self.r - .1 and child.pos[
1] < self.r - .1 and child.name != "Temp":
self.add(mb.clone(child))
del s
def __init__(self, nano, n, box, seed=12345):
super(PatchyBox, self).__init__()
if type(nano) is not list:
nano = [nano]
if type(n) is not list:
n = [n]
# Define positions for nanoparticles (use points to speed
# this up)
point_rep = mb.Particle(name='point0')
d_vdw = max([
max(nano[0].xyz[:, dim]) - min(nano[0].xyz[:, dim])
for dim in range(3)
])
point_box = mb.fill_box(point_rep,
n[0],
box,
overlap=d_vdw + 0.5,
edge=d_vdw / 2 + 0.25,
seed=seed)
for i, (np_proto, np_n) in enumerate(zip(nano[1:], n[1:])):
point_rep = mb.Particle(name='point{:d}'.format(i + 1))
d_vdw = max([
max(np_proto.xyz[:, dim]) - min(np_proto.xyz[:, dim])
for dim in range(3)
])
point_box = mb.solvate(solute=point_box,
solvent=point_rep,
n_solvent=np_n,
box=box,
overlap=d_vdw + 0.5,
edge=d_vdw / 2 + 0.25,
seed=seed)
self.periodicity = box.lengths
random.seed(seed)
# Replicate the nanoparticle at the defined positions
for particle in point_box.particles():
nano_index = int(particle.name.strip('point'))
nano_clone = mb.clone(nano[nano_index])
nano_clone.spin(
random.random() * 2 * np.pi,
np.array([random.random(),
random.random(),
random.random()]) - 0.5)
#mb.translate_to(nano_clone, particle.pos)
nano_clone.translate_to(particle.pos)
self.add(nano_clone)
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 test_solvate_multiple(self, methane, ethane, h2o):
init_box = mb.fill_box(methane, 2, box=[4, 4, 4])
solvated = mb.solvate(init_box, [ethane, h2o], [20, 20], box=[4, 4, 4])
assert solvated.n_particles == 2 * 5 + 20 * 8 + 20 * 3
assert len(solvated.children) == 41
def test_solvate(self, ethane, h2o):
n_solvent = 100
solvated = mb.solvate(ethane, h2o, n_solvent=n_solvent, box=[4, 4, 4])
assert solvated.n_particles == 8 + n_solvent * 3
assert solvated.n_bonds == 7 + n_solvent * 2
assert ethane.parent == None
def test_solvate_multiple(self, methane, ethane, h2o):
init_box = mb.fill_box(methane, 2, box=[4, 4, 4])
solvated = mb.solvate(init_box, [ethane, h2o], [20, 20], box=[4, 4, 4])
assert solvated.n_particles == 2*5 + 20*8 + 20*3
assert len(solvated.children) == 41
def test_solvate(self, ethane, h2o):
n_solvent = 100
solvated = mb.solvate(ethane, h2o, n_solvent=n_solvent, box=[4, 4, 4])
assert solvated.n_particles == 8 + n_solvent * 3
assert solvated.n_bonds == 7 + n_solvent * 2
def test_solvate(self, ethane, h2o):
solvated = mb.solvate(ethane, h2o, n_solvent=100, box=[4, 4, 4])
assert solvated.n_particles == 8 + 100 * 3
assert solvated.n_bonds == 7 + 100 * 2
# Bilayer needs to be shifted to fit inside the box for gromacs (can't have any negative coordinates)
mb.translate(system, [
np.abs(systembox.mins[0]),
np.abs(systembox.mins[1]),
np.abs(systembox.mins[2])
])
# Shrink the x and y dimensions of the box to prevent packmol from shoving atoms in weird locations
cross_area = (n_x * spacing - 1) * (n_y * spacing - 1)
leaflet_water_z = n_solvent_per_layer * 2.66602458e-2 / cross_area
# Redefine the box to account for shifted coordinates and add extra space in z-direcction
smallbox = mb.Box(
mins=[0, 0, systembox.mins[2] - leaflet_water_z],
maxs=[n_x * spacing, n_y * spacing, systembox.maxs[2] + leaflet_water_z])
# The solvate box will have a reduced cross-sectional area to prevent waters in strange locations
solvatebox = mb.Box(
mins=[0.5, 0.5, smallbox.mins[2]],
maxs=[smallbox.maxs[0] - 0.5, smallbox.maxs[1] - 0.5, smallbox.maxs[2]])
# Solvate system
system = mb.solvate(system, H2O(), 2 * n_solvent_per_layer, solvatebox)
# Bilayer needs to be shifted to fit inside the box for gromacs (can't have any negative coordinates)
mb.translate(system, [
np.abs(smallbox.mins[0]),
np.abs(smallbox.mins[1]),
np.abs(smallbox.mins[2])
])
system.save('mbuild_bilayer.gro', box=smallbox, overwrite=True)
def main():
"""Solvate an ethane molecule in a Box of water. """
ethane = Ethane()
water = H2O()
return mb.solvate(ethane, water, 500, box=[2, 2, 2])