def build_monolayer(chain_length, n_molecules, **kwargs):
from mbuild.examples import AlkaneMonolayer
pattern = mb.Random2DPattern(n_molecules)
monolayer = AlkaneMonolayer(pattern, tile_x=1, tile_y=1, chain_length=chain_length)
monolayer.name = 'alkane_n-{}_l-{}'.format(n_molecules, chain_length)
mb.translate(monolayer, [0, 0, 2])
return monolayer
def build_monolayer(chain_length, n_molecules, **kwargs):
from mbuild.examples import AlkaneMonolayer
pattern = mb.Random2DPattern(n_molecules)
monolayer = AlkaneMonolayer(pattern, tile_x=1, tile_y=1, chain_length=chain_length)
monolayer.name = 'alkane_n-{}_l-{}'.format(n_molecules, chain_length)
mb.translate(monolayer, [0, 0, 2])
box = monolayer.boundingbox
monolayer.periodicity += np.array([0, 0, 5 * box.lengths[2]])
return monolayer
def build_monolayer(chain_length, n_molecules, **kwargs):
from mbuild.examples import AlkaneMonolayer
pattern = mb.Random2DPattern(n_molecules)
monolayer = AlkaneMonolayer(pattern,
tile_x=1,
tile_y=1,
chain_length=chain_length)
monolayer.name = 'alkane_n-{}_l-{}'.format(n_molecules, chain_length)
mb.translate(monolayer, [0, 0, 2])
box = monolayer.boundingbox
monolayer.periodicity += np.array([0, 0, 5 * box.lengths[2]])
return monolayer
def build_monolayer(chain_length, n_molecules, pattern_class, **kwargs):
from mbuild.examples import AlkaneMonolayer
if pattern_class is mb.Random2DPattern:
if n_molecules in used_random_patterns:
pattern = used_random_patterns[n_molecules]
else:
pattern = pattern_class(n_molecules)
pattern_name = 'rand'
if pattern_class is mb.Grid2DPattern:
pattern = pattern_class(int(np.sqrt(n_molecules)),
int(np.sqrt(n_molecules)))
pattern_name = 'grid'
bot = AlkaneMonolayer(pattern,
tile_x=1,
tile_y=1,
chain_length=chain_length)
mb.translate(bot, [0, 0, 2])
bot_box = bot.boundingbox
bot_of_bot = bot_box.mins[2]
bot_rigid = [
i + 1 for i, a in enumerate(bot.particles())
if (a.pos[2] < bot_of_bot + 0.05) and a.name == 'Si'
]
n_particles = bot.n_particles
top_rigid = [i + n_particles for i in bot_rigid]
top = mb.clone(bot)
mb.spin_y(top, np.pi)
top_of_bot = bot_box.maxs[2]
bot_of_top = top.boundingbox.mins[2]
mb.translate(top, [0, 0, top_of_bot - bot_of_top + 0.5])
monolayer = mb.Compound([bot, top])
monolayer.name = 'alkane_n-{}_l-{}-{}'.format(n_molecules, chain_length,
pattern_name)
rigid_groups = {'bot': bot_rigid, 'top': top_rigid}
return monolayer, rigid_groups
def alkane_monolayer(self):
from mbuild.examples import AlkaneMonolayer
pattern = mb.Random2DPattern(50, seed=1)
monolayer = AlkaneMonolayer(pattern=pattern)
return monolayer