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_apply_residues():
import mbuild as mb
from mbuild.examples import Ethane
ethane = Ethane()
opls = Forcefield(name='oplsaa')
typed = opls.apply(ethane, residues='CH3')
assert len([res for res in typed.residues if res.name == 'CH3']) == 2
def ethane(self):
from mbuild.examples import Ethane
return Ethane()
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)
if not is_leaf(real_thing):
# create labels
for label, part in real_thing.labels.items():
if isinstance(part, list):
# TODO support lists with labels
continue
if part in memo:
memo[real_thing].labels[label] = memo[part]
# recurse
for part in real_thing.children:
_create_proxy_labels(part, memo)
if __name__ == '__main__':
from mbuild.examples import Ethane
c = Ethane()
# c = create_proxy(c)
# p = create_proxy(c, leaf_classes=mbuild.lib.moieties.ch3.CH3)
p = create_proxy(c)
print("Top level proxy object: {}".format(p))
print("Parts of top level proxy object:")
for part in p.children:
print(" {}".format(part))
print("Leaves of top level proxy object:")
for particle in p.particles():
print(" {}".format(particle.name))