def test_independent_residues_molecules():
"""Test to see that _check_independent_residues works for molecules."""
butane = Alkane(4)
structure = butane.to_parmed()
topo, NULL = generate_topology(structure)
assert _check_independent_residues(topo)
structure = butane.to_parmed(residues=['RES', 'CH3'])
topo, NULL = generate_topology(structure)
assert not _check_independent_residues(topo)
def test_independent_residues_molecules():
"""Test to see that _check_independent_residues works for molecules."""
butane = Alkane(4)
structure = butane.to_parmed()
topo, NULL = generate_topology(structure)
assert _check_independent_residues(topo)
structure = butane.to_parmed(residues=['RES', 'CH3'])
topo, NULL = generate_topology(structure)
assert not _check_independent_residues(topo)
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_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 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_conversions(self):
# Check to see if we can correctly spawn engine simulations
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.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance': 10,
'ref_energy': 1 / 4.184
})
assert df is not None
def alkyl(self):
from mbuild.examples import Alkane
return Alkane(2, cap_front=True, cap_end=False)
def test_mbuild_examples(self):
import mbuild as mb
from mbuild.examples import (Alkane, Methane, Ethane, PMPCLayer,
AlkaneMonolayer)
import foyer
for i in range(4, 20):
my_alkane = Alkane(n=i)
ff = foyer.Forcefield(name='oplsaa')
structure = ff.apply(my_alkane)
bbox = my_alkane.boundingbox
bbox.lengths *= 10
if any(bbox.lengths < 10):
bbox.lengths = [100, 100, 100]
structure.box = [
bbox.lengths[0], bbox.lengths[1], bbox.lengths[2], 90, 90, 90
]
structure.combining_rule = 'lorentz'
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance':
10,
'ref_energy':
1 / 4.184
})
print('Alkane, n={}'.format(i))
print(energies)
print('=' * 20)
eth = Ethane()
structure = ff.apply(eth)
bbox = eth.boundingbox
bbox.lengths *= 10
if any(bbox.lengths < 10):
bbox.lengths = [100, 100, 100]
structure.box = [
bbox.lengths[0], bbox.lengths[1], bbox.lengths[2], 90, 90, 90
]
structure.combining_rule = 'lorentz'
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance': 10,
'ref_energy':
1 / 4.184
})
print("Ethane")
print(energies)
print('=' * 20)
methan = Methane()
structure = ff.apply(methan)
bbox = methan.boundingbox
bbox.lengths *= 10
if any(bbox.lengths < 10):
bbox.lengths = [100, 100, 100]
structure.box = [
bbox.lengths[0], bbox.lengths[1], bbox.lengths[2], 90, 90, 90
]
structure.combining_rule = 'lorentz'
energies = commpare.spawn_engine_simulations(structure,
hoomd_kwargs={
'ref_distance': 10,
'ref_energy':
1 / 4.184
})
print("Methane")
print(energies)
print('=' * 20)
def octane(self):
from mbuild.examples import Alkane
return Alkane(8, cap_front=True, cap_end=True)
def test_remove_port(self):
from mbuild.examples import Alkane
butane = Alkane(n=4)
butane.remove(butane[-1])
box = mb.fill_box(butane, n_compounds=10, density=1)