import signac
import hoomd
import hoomd.md

project = signac.init_project('hoomd-lennard-jones')

for kT in (0.1, 1.0, 2.0):
    with project.open_job({'kT': kT, 'seed': 42}) as job:
        hoomd.context.initialize()
        hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=2.0), n=5)
        nl = hoomd.md.nlist.cell()
        lj = hoomd.md.pair.lj(r_cut=2.5, nlist=nl)
        lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
        hoomd.md.integrate.mode_standard(dt=0.005)
        all = hoomd.group.all()
        hoomd.md.integrate.langevin(group=all, kT=job.sp.kT, seed=job.sp.seed)
        hoomd.analyze.log(filename="log-output.log",
                          quantities=['potential_energy', 'temperature', 'pressure'],
                          period=100,
                          overwrite=True)
        hoomd.dump.gsd("trajectory.gsd", period=2e3, group=all, overwrite=True)
        hoomd.run(1e4)

ff14000d3472861ce68509c63dae0decccd6d6b4
<mask token>

<mask token>
for kT in (0.1, 1.0, 2.0):
    with project.open_job({'kT': kT, 'seed': 42}) as job:
        hoomd.context.initialize()
        hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=2.0), n=5)
        nl = hoomd.md.nlist.cell()
        lj = hoomd.md.pair.lj(r_cut=2.5, nlist=nl)
        lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
        hoomd.md.integrate.mode_standard(dt=0.005)
        all = hoomd.group.all()
        hoomd.md.integrate.langevin(group=all, kT=job.sp.kT, seed=job.sp.seed)
        hoomd.analyze.log(filename='log-output.log', quantities=[
            'potential_energy', 'temperature', 'pressure'], period=100,
            overwrite=True)
        hoomd.dump.gsd('trajectory.gsd', period=2000.0, group=all,
            overwrite=True)
        hoomd.run(10000.0)

<mask token>
project = signac.init_project('hoomd-lennard-jones')
for kT in (0.1, 1.0, 2.0):
    with project.open_job({'kT': kT, 'seed': 42}) as job:
        hoomd.context.initialize()
        hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=2.0), n=5)
        nl = hoomd.md.nlist.cell()
        lj = hoomd.md.pair.lj(r_cut=2.5, nlist=nl)
        lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
        hoomd.md.integrate.mode_standard(dt=0.005)
        all = hoomd.group.all()
        hoomd.md.integrate.langevin(group=all, kT=job.sp.kT, seed=job.sp.seed)
        hoomd.analyze.log(filename='log-output.log', quantities=[
            'potential_energy', 'temperature', 'pressure'], period=100,
            overwrite=True)
        hoomd.dump.gsd('trajectory.gsd', period=2000.0, group=all,
            overwrite=True)
        hoomd.run(10000.0)

import signac
import hoomd
import hoomd.md
project = signac.init_project('hoomd-lennard-jones')
for kT in (0.1, 1.0, 2.0):
    with project.open_job({'kT': kT, 'seed': 42}) as job:
        hoomd.context.initialize()
        hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=2.0), n=5)
        nl = hoomd.md.nlist.cell()
        lj = hoomd.md.pair.lj(r_cut=2.5, nlist=nl)
        lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
        hoomd.md.integrate.mode_standard(dt=0.005)
        all = hoomd.group.all()
        hoomd.md.integrate.langevin(group=all, kT=job.sp.kT, seed=job.sp.seed)
        hoomd.analyze.log(filename='log-output.log', quantities=[
            'potential_energy', 'temperature', 'pressure'], period=100,
            overwrite=True)
        hoomd.dump.gsd('trajectory.gsd', period=2000.0, group=all,
            overwrite=True)
        hoomd.run(10000.0)

import signac
import hoomd
import hoomd.md

project = signac.init_project('hoomd-lennard-jones')

for kT in (0.1, 1.0, 2.0):
    with project.open_job({'kT': kT, 'seed': 42}) as job:
        hoomd.context.initialize()
        hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=2.0), n=5)
        nl = hoomd.md.nlist.cell()
        lj = hoomd.md.pair.lj(r_cut=2.5, nlist=nl)
        lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
        hoomd.md.integrate.mode_standard(dt=0.005)
        all = hoomd.group.all()
        hoomd.md.integrate.langevin(group=all, kT=job.sp.kT, seed=job.sp.seed)
        hoomd.analyze.log(filename="log-output.log",
                          quantities=['potential_energy', 'temperature', 'pressure'],
                          period=100,
                          overwrite=True)
        hoomd.dump.gsd("trajectory.gsd", period=2e3, group=all, overwrite=True)
        hoomd.run(1e4)
