def run_adsorption(job):
"""Run adsorption simulation for the given statepoint"""
import mbuild
import unyt as u
from mosdef_slitpore.utils.cassandra_runners import run_adsorption
pore_width = 1.0 * u.nm
temperature = job.sp.T * u.K
mu = job.sp.mu * u.kJ / u.mol
nsteps_gcmc = job.sp.nsteps_gcmc
seed1 = job.sp.seed1
seed2 = job.sp.seed2
# Create empty pore system
empty_pore = mbuild.recipes.GraphenePore(
pore_length=1.0,
pore_depth=1.1,
pore_width=pore_width.to_value("nm"),
n_sheets=1,
slit_pore_dim=2,
)
# Translate to centered at 0,0,0 and make box larger in z
box_center = empty_pore.periodicity / 2.0
empty_pore.translate(-box_center)
empty_pore.periodicity[2] = 2.0
# Run simulation from inside job dir
# Here we lower the vdw/charge cutoffs bc of small box
with job:
run_adsorption(
empty_pore,
pore_width,
temperature,
mu,
nsteps_gcmc,
seeds=[seed1, seed2],
vdw_cutoff=4.9 * u.angstrom,
charge_cutoff=4.9 * u.angstrom,
)
def run_adsorption(job):
"""Run adsorption simulation for the given statepoint"""
import mbuild
import unyt as u
from mosdef_slitpore.utils.cassandra_runners import run_adsorption
pore_width = 1.6 * u.nm
temperature = job.sp.T * u.K
mu = job.sp.mu * u.kJ / u.mol
nsteps_gcmc = job.sp.nsteps_gcmc
seed1 = job.sp.seed1
seed2 = job.sp.seed2
# Create empty pore system
empty_pore = mbuild.recipes.GraphenePore(
pore_length=3.0,
pore_depth=3.0,
pore_width=pore_width.to_value("nm"),
n_sheets=3,
slit_pore_dim=2,
)
# Translate to centered at 0,0,0 and make box larger in z
empty_pore.translate(-empty_pore.center)
empty_pore.periodicity[2] = 6.0
# Run simulation from inside job dir
with job:
run_adsorption(empty_pore,
pore_width,
temperature,
mu,
nsteps_gcmc,
seeds=[seed1, seed2])