def test_create_semi_rigid_bodies_hierarchy(self, benzene_from_parts):
n_benzenes = 10
filled = mb.fill_box(benzene_from_parts,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.name = 'Benzene box'
filled2 = mb.clone(filled)
compound = mb.Compound(subcompounds=[filled, filled2])
compound.label_rigid_bodies(discrete_bodies='Benzene box')
assert compound.max_rigid_id == 1
assert filled.max_rigid_id == 0
assert filled2.max_rigid_id == 1
assert len(list(compound.rigid_particles())) == n_benzenes * 2 * 12
compound.unlabel_rigid_bodies()
compound.label_rigid_bodies(discrete_bodies='Benzene', rigid_particles='C')
assert compound.max_rigid_id == (n_benzenes*2) - 1
assert filled.max_rigid_id == n_benzenes - 1
assert filled2.max_rigid_id == (n_benzenes*2) - 1
assert len(list(compound.rigid_particles())) == n_benzenes * 2 * 6
assert len(list(filled.rigid_particles())) == n_benzenes * 6
assert len(list(filled2.rigid_particles())) == n_benzenes * 6
compound.unlabel_rigid_bodies()
compound.label_rigid_bodies(discrete_bodies='CH')
assert compound.max_rigid_id == (n_benzenes*2*6) - 1
assert filled.max_rigid_id == (n_benzenes*6) - 1
assert filled2.max_rigid_id == (n_benzenes*2*6) - 1
assert len(list(compound.rigid_particles())) == n_benzenes * 2 * 12
assert len(list(filled.rigid_particles())) == n_benzenes * 12
assert len(list(filled2.rigid_particles())) == n_benzenes * 12
def test_fill_box_aspect_ratio(self, h2o):
filled = mb.fill_box(h2o,
n_compounds=1000,
density=1000,
aspect_ratio=[1, 2, 1])
assert np.isclose(filled.box.lengths[0] / filled.box.lengths[1], 0.5)
assert np.isclose(filled.box.lengths[1] / filled.box.lengths[2], 2)
def test_fill_box_aspect_ratio(self, h2o):
filled = mb.fill_box(h2o,
n_compounds=1000,
density=1000,
aspect_ratio=[1, 2, 1])
assert filled.periodicity[0] / filled.periodicity[1] == 0.5
assert filled.periodicity[1] / filled.periodicity[2] == 2
def build_ethane_box(box, n_molecules):
from mbuild.examples import Ethane
import mbuild as mb
ethane = Ethane()
full_box = mb.fill_box(ethane, n_molecules, box)
full_box.name = '{}_ethanes'.format(n_molecules)
return full_box
def test_to_more_pybel_residues(self, methane, ethane):
box = mb.fill_box([methane, ethane], n_compounds=[3,3],
box=mb.Box([10,10,10]))
pybel_mol = box.to_pybel(box=None, residues=['Ethane', 'Methane'])
pybel_mol_resnames = {a.name for a in pybel_mol.residues}
assert 'Ethane' in pybel_mol_resnames
assert 'Methane' in pybel_mol_resnames
def test_label_rigid_bodies_duplicate_warn(self, rigid_benzene):
with pytest.warns(UserWarning):
n_benzenes = 10
filled = mb.fill_box(rigid_benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies='Benzene')
def __init__(self, chain_length, n_chains, density):
"""Initialize an AlkaneBox Compound.
Parameters
----------
chain_length : int
Length of the alkane chains (in number of carbons)
n_chains : int
Number of chains to place in the box
density : float
Density (in kg/m^3) at which the system should be created
"""
super(AlkaneBox, self).__init__()
# Create alkane chain prototype using the class above
chain = Alkane(chain_length=chain_length)
# Generate a more relaxed structure
chain.energy_minimization()
# Fill a box with chains at a user-defined density
box_of_alkanes = mb.fill_box(compound=chain,
n_compounds=n_chains,
density=density)
# Rename all chains to `Alkane`, this speeds up the atom-typing process
for child in box_of_alkanes.children:
child.name = 'Alkane'
self.add(box_of_alkanes)
def test_rotate(self, h2o):
filled = mb.fill_box(h2o, 2, box=[1, 1, 1], fix_orientation=True)
w0 = filled.xyz[:3]
w1 = filled.xyz[3:]
# Translate w0 and w1 to COM
w0 -= w0.sum(0) / len(w0)
w1 -= w1.sum(0) / len(w1)
assert np.isclose(w0, w1).all()
def test_fill_box_compound_ratio(self, h2o, ethane):
filled = mb.fill_box(compound=[h2o, ethane],
density=800,
compound_ratio=[2, 1],
box=[2, 2, 2, 4, 4, 4])
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_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_rotate(self, h2o):
filled = mb.fill_box(h2o, 2, box=[1, 1, 1], fix_orientation=True)
w0 = filled.xyz[:3]
w1 = filled.xyz[3:]
# Translate w0 and w1 to COM
w0 -= w0.sum(0) / len(w0)
w1 -= w1.sum(0) / len(w1)
assert np.isclose(w0, w1).all()
def box_of_benzenes(self, benzene):
n_benzenes = 10
benzene.name = 'Benzene'
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies='Benzene', rigid_particles='C')
return filled
def test_no_rotate(self, h2o):
filled = mb.fill_box([h2o, h2o], [1, 1], box=[1, 1, 1], fix_orientation=[False, True])
w0 = filled.xyz[:3]
w1 = filled.xyz[3:]
# Translate w0 and w1 to COM
w0 -= w0.sum(0) / len(w0)
w1 -= w1.sum(0) / len(w1)
assert np.isclose(w0, w1).all() is not True
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 box_of_benzenes(self, benzene):
n_benzenes = 10
benzene.name = 'Benzene'
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies='Benzene', rigid_particles='C')
return filled
def test_no_rotate(self, h2o):
filled = mb.fill_box([h2o, h2o], [1, 1], box=[1, 1, 1], fix_orientation=[False, True])
w0 = filled.xyz[:3]
w1 = filled.xyz[3:]
# Translate w0 and w1 to COM
w0 -= w0.sum(0) / len(w0)
w1 -= w1.sum(0) / len(w1)
assert np.isclose(w0, w1).all() is not True
def test_box_dimensions(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.save(filename='benzene.hoomdxml')
for atom in mb.load('benzene.hoomdxml'):
assert atom.pos.max() < 20
assert atom.pos.min() > -20
def test_empty_initial_snapshot(self):
hoomd = import_("hoomd")
hoomd_snapshot = import_("mbuild.formats.hoomd_snapshot")
part = mb.Compound(name='Ar')
box = mb.fill_box(part, n_compounds=10, box=mb.Box([5, 5, 5]))
init_snap = hoomd.data.make_snapshot(N=0, box=hoomd.data.boxdim(L=10))
with pytest.raises(RuntimeError):
snap, _ = hoomd_snapshot.to_hoomdsnapshot(box,
hoomd_snapshot=init_snap)
def test_save_non_sequential_rigid_ids(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies='Benzene')
filled.children[0]._increment_rigid_ids(increment=3)
with pytest.warns(UserWarning):
filled.save('benzene-box.hoomdxml')
def test_save_non_sequential_rigid_ids(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies="Benzene")
filled.children[0]._increment_rigid_ids(increment=3)
with pytest.warns(UserWarning):
filled.save("benzene-box.hoomdxml")
def test_box_dimensions(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.save(filename='benzene.hoomdxml')
for atom in mb.load('benzene.hoomdxml'):
assert atom.pos.max() < 20
assert atom.pos.min() > -20
def test_delete_body_multiple(self, rigid_benzene):
n_benzenes = 10
filled = mb.fill_box(rigid_benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.remove([filled.children[0], filled.children[1]])
assert filled.max_rigid_id == n_benzenes - 3
assert len(list(filled.rigid_particles())) == (n_benzenes - 2) * rigid_benzene.n_particles
def test_particles_to_snapshot(self):
hoomd_snapshot = import_("mbuild.formats.hoomd_snapshot")
part = mb.Compound(name='Ar')
box = mb.fill_box(part, n_compounds=10, box=mb.Box([5, 5, 5]))
snap, _ = hoomd_snapshot.to_hoomdsnapshot(box)
assert snap.particles.N == 10
assert snap.bonds.N == 0
assert snap.angles.N == 0
def test_multiple_molecules(self, ethane):
n_ethane = 2
ethane.name = 'Ethane'
filled = mb.fill_box(ethane,n_compounds=n_ethane,box=[0,0,0,4,4,4])
with pytest.raises(ValueError,
match=r'Not all components of the molecule'):
filled.save(filename='box-ethane-opls.mcf',
forcefield_name='oplsaa',angle_style='harmonic',
dihedral_style='opls')
def test_label_semi_rigid_bodies_after_fill(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies='Benzene', rigid_particles='C')
assert filled.max_rigid_id == n_benzenes - 1
assert len(list(filled.rigid_particles())) == n_benzenes * 6
def initialize(job):
"Inialize the simulation"
alkane = Alkane(job.statepoint()['C_n'])
n_alkane = 200
# A cleaner packing approach would involve pull #372
system_box = mb.Box([4, 4, 4])
system = mb.fill_box(compound=alkane, n_compounds=n_alkane, box=system_box)
system.save('init.gro', overwrite=True)
system.save('init.top', forcefield_name='oplsaa', overwrite=True)
def test_delete_body_semi_rigid(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies='Benzene', rigid_particles='C')
filled.remove(filled.children[0])
assert filled.max_rigid_id == n_benzenes - 2
assert len(list(filled.rigid_particles())) == (n_benzenes - 1) * 6
def test_delete_body_particle_by_particle(self, rigid_benzene):
n_benzenes = 10
filled = mb.fill_box(rigid_benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
for particle in filled.children[0].particles():
filled.remove(particle)
assert filled.max_rigid_id == n_benzenes - 2
assert len(list(filled.rigid_particles())) == (n_benzenes - 1) * rigid_benzene.n_particles
def test_fill_box_rigid(self, rigid_benzene):
n_benzenes = 10
filled = mb.fill_box(rigid_benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
assert filled.contains_rigid is True
assert filled.rigid_id is None
assert filled.max_rigid_id == n_benzenes - 1
assert len(list(filled.rigid_particles())) == n_benzenes * rigid_benzene.n_particles
def test_opls(self):
eth = Alkane(n=10)
cmpd = mb.fill_box(eth, n_compounds=10, box=[10, 10, 10])
ff = foyer.Forcefield(name='oplsaa')
structure = ff.apply(cmpd)
df = commpare.openmm.build_run_measure_openmm(structure)
assert 'bond' in df
assert 'angle' in df
assert 'dihedral' in df
assert 'nonbond' in df
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 _topology(n_sites=100):
ar = mb.Compound(name='Ar')
packed_system = mb.fill_box(
compound=ar,
n_compounds=n_sites,
box=mb.Box([3, 3, 3]),
)
return packed_system
def test_delete_body_multiple(self, rigid_benzene):
n_benzenes = 10
filled = mb.fill_box(rigid_benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.remove([filled.children[0], filled.children[1]])
assert filled.max_rigid_id == n_benzenes - 3
assert (len(list(filled.rigid_particles())) == (n_benzenes - 2) *
rigid_benzene.n_particles)
def test_label_semi_rigid_bodies_after_fill(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies="Benzene",
rigid_particles="C")
assert filled.max_rigid_id == n_benzenes - 1
assert len(list(filled.rigid_particles())) == n_benzenes * 6
def test_particles_to_snapshot(self):
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
part = mb.Compound(name="Ar")
box = mb.Box(lengths=[5, 5, 5], angles=[90, 90, 90])
system = mb.fill_box(part, n_compounds=10, box=box)
snap, _ = to_hoomdsnapshot(system)
assert snap.particles.N == 10
assert snap.bonds.N == 0
assert snap.angles.N == 0
def test_fill_box_semi_rigid(self, benzene):
n_benzenes = 10
benzene.label_rigid_bodies(rigid_particles='C')
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
assert filled.contains_rigid is True
assert filled.rigid_id is None
assert filled.max_rigid_id == n_benzenes - 1
assert len(list(filled.rigid_particles())) == n_benzenes * 6
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_empty_initial_snapshot(self):
import hoomd
from mbuild.formats.hoomd_snapshot import to_hoomdsnapshot
part = mb.Compound(name="Ar")
box = mb.Box(lengths=[5, 5, 5], angles=[90, 90, 90])
system = mb.fill_box(part, n_compounds=10, box=box)
init_snap = hoomd.data.make_snapshot(N=0, box=hoomd.data.boxdim(L=10))
with pytest.raises(RuntimeError):
snap, _ = to_hoomdsnapshot(system, hoomd_snapshot=init_snap)
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])
def test_delete_body_semi_rigid(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies="Benzene",
rigid_particles="C")
filled.remove(filled.children[0])
assert filled.max_rigid_id == n_benzenes - 2
assert len(list(filled.rigid_particles())) == (n_benzenes - 1) * 6
def test_delete_body_particle_by_particle(self, rigid_benzene):
n_benzenes = 10
filled = mb.fill_box(rigid_benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
for particle in list(filled.children[0].particles()):
filled.remove(particle)
assert filled.max_rigid_id == n_benzenes - 2
assert (len(list(filled.rigid_particles())) == (n_benzenes - 1) *
rigid_benzene.n_particles)
def test_fill_box_semi_rigid(self, benzene):
n_benzenes = 10
benzene.label_rigid_bodies(rigid_particles="C")
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
assert filled.contains_rigid is True
assert filled.rigid_id is None
assert filled.max_rigid_id == n_benzenes - 1
assert len(list(filled.rigid_particles())) == n_benzenes * 6
def test_fill_box_rigid(self, rigid_benzene):
n_benzenes = 10
filled = mb.fill_box(rigid_benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
assert filled.contains_rigid is True
assert filled.rigid_id is None
assert filled.max_rigid_id == n_benzenes - 1
assert (len(list(filled.rigid_particles())) == n_benzenes *
rigid_benzene.n_particles)
def test_label_rigid_bodies_after_fill(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies="Benzene")
assert filled.contains_rigid is True
assert filled.rigid_id is None
assert filled.max_rigid_id == n_benzenes - 1
assert (len(list(filled.rigid_particles())) == n_benzenes *
benzene.n_particles)
def test_opls(self):
eth = Alkane(n=10)
cmpd = mb.fill_box(eth, n_compounds=10, box=[10, 10, 10])
ff = foyer.Forcefield(name='oplsaa')
structure = ff.apply(cmpd)
df = commpare.hoomd.build_run_measure_hoomd(structure,
ref_energy=1 / 4.184,
ref_distance=10)
assert 'bond' in df
assert 'angle' in df
assert 'dihedral' in df
assert 'nonbond' in df
def test_remove_from_box(self, ethane):
n_ethanes = 5
box = mb.fill_box(ethane, n_ethanes, [3, 3, 3])
box.remove(box.children[3])
n_ethanes -= 1
assert box.n_particles == n_ethanes * ethane.n_particles
assert len(box.children) == n_ethanes
assert box.n_bonds == n_ethanes * ethane.n_bonds
assert len([meth.referenced_ports()
for eth in box.children
for meth in eth.children]) == 2 * n_ethanes
def test_create_semi_rigid_bodies_filled_no_increment(self, benzene_from_parts):
n_benzenes = 10
filled = mb.fill_box(benzene_from_parts,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies='Benzene', rigid_particles='C')
filled2 = mb.clone(filled)
filled.add(filled2, reset_rigid_ids=False)
assert filled.max_rigid_id == n_benzenes - 1
assert len(list(filled.rigid_particles())) == n_benzenes * 2 * 6
for rigid_id in range(n_benzenes):
assert len(list(filled.rigid_particles(rigid_id=rigid_id))) == 12
def test_label_rigid_bodies_list(self, benzene):
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.children[0].name = 'Benzene0'
filled.children[1].name = 'Benzene1'
filled.label_rigid_bodies(discrete_bodies=['Benzene0', 'Benzene1'])
assert filled.contains_rigid is True
assert filled.rigid_id is None
assert filled.max_rigid_id == 1
assert len(list(filled.rigid_particles())) == 2 * benzene.n_particles
def solvate_bilayer(self):
"""Solvate the constructed bilayer. """
solvent_number_density = self.solvent.n_particles / np.prod(self.solvent.periodicity)
lengths = self.lipid_box.lengths
water_box_z = self.solvent_per_layer / (lengths[0] * lengths[1] * solvent_number_density)
mins = self.lipid_box.mins
maxs = self.lipid_box.maxs
bilayer_solvent_box = mb.Box(mins=[mins[0], mins[1], maxs[2]],
maxs=[maxs[0], maxs[1], maxs[2] + 2 * water_box_z])
self.solvent_components.add(mb.fill_box(self.solvent, bilayer_solvent_box))
def test_box_dimensions(self, benzene):
import gsd
n_benzenes = 10
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.save(filename='benzene.gsd')
gsd_file = gsd.pygsd.GSDFile(open('benzene.gsd', 'rb'))
frame = gsd.hoomd.HOOMDTrajectory(gsd_file).read_frame(0)
positions = frame.particles.position.astype(float)
for coords in positions:
assert coords.max() < 20
assert coords.min() > -20
def test_delete_body_all(self, rigid_benzene):
n_benzenes = 10
filled = mb.fill_box(rigid_benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
for i, child in enumerate(filled.children[:-1]):
filled.remove(child)
assert filled.max_rigid_id == n_benzenes - 1 - (i + 1)
assert len(list(filled.rigid_particles())) == (n_benzenes - (i + 1)) * rigid_benzene.n_particles
assert filled.contains_rigid is True
filled.remove(filled.children[0])
assert filled.contains_rigid is False
assert filled.max_rigid_id is None
def test_rigid(self, benzene):
n_benzenes = 10
benzene.name = 'Benzene'
filled = mb.fill_box(benzene,
n_compounds=n_benzenes,
box=[0, 0, 0, 4, 4, 4])
filled.label_rigid_bodies(discrete_bodies='Benzene', rigid_particles='C')
filled.save(filename='benzene.hoomdxml')
xml_file = xml.etree.ElementTree.parse('benzene.hoomdxml').getroot()
body_text = xml_file[0].find('body').text
rigid_bodies = [int(body) for body in body_text.split('\n') if body]
for body_id in range(10):
assert rigid_bodies.count(body_id) == 6
assert rigid_bodies.count(-1) == n_benzenes * 6
def test_packmol_warning(self, h2o):
with pytest.warns(UserWarning):
filled = mb.fill_box(h2o, n_compounds=10, box=[1, 1, 1], overlap=10)
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 test_fill_box_density_box(self, h2o):
filled = mb.fill_box(h2o, n_compounds=1000, density=1000)
assert [3.1042931 < period < 3.1042932 for period in filled.periodicity]
def test_fill_box_compound_ratio(self, h2o, ethane):
filled = mb.fill_box(compound=[h2o, ethane], density=800,
compound_ratio=[2, 1], box=[2, 2, 2, 4, 4, 4])
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_box_density_n_compounds(self, h2o):
filled = mb.fill_box(h2o, density=1000,
box=mb.Box([3.1042931, 3.1042931, 3.1042931]))
assert filled.n_particles == 3000
def test_fill_box_aspect_ratio(self, h2o):
filled = mb.fill_box(h2o, n_compounds=1000,
density=1000, aspect_ratio=[1, 2, 1])
assert filled.periodicity[0]/filled.periodicity[1] == 0.5
assert filled.periodicity[1]/filled.periodicity[2] == 2
def test_packmol_error(self, h2o):
with pytest.raises(RuntimeError):
filled = mb.fill_box(h2o, n_compounds=10, box=[0, 0, 0])
def test_packmol_log_error(self, h2o):
try:
filled = mb.fill_box(h2o, n_compounds=10, box=[0, 0, 0])
except(RuntimeError):
with open("log.txt", "r") as logfile:
assert "ERROR" in logfile.read()
