def test_lj_energy(self):
model_dir = build_examples.lj_graph(9 - 1, self.tmp)
with hoomd.htf.tfcompute(model_dir) as tfcompute:
hoomd.context.initialize()
N = 3 * 3
NN = N - 1
T = 10
rcut = 5.0
system = hoomd.init.create_lattice(
unitcell=hoomd.lattice.sq(a=4.0),
n=[3, 3])
nlist = hoomd.md.nlist.cell(check_period=1)
hoomd.md.integrate.mode_standard(dt=0.001)
hoomd.md.integrate.nve(group=hoomd.group.all(
)).randomize_velocities(seed=1, kT=0.8)
log = hoomd.analyze.log(filename=None,
quantities=['potential_energy',
'kinetic_energy'], period=1)
tfcompute.attach(nlist, r_cut=rcut)
energy = []
for i in range(T):
hoomd.run(250)
energy.append(log.query('potential_energy'
) + log.query('kinetic_energy'))
if i > 1:
np.testing.assert_allclose(energy[-1],
energy[-2], atol=1e-3)
def test_lj_pressure(self):
# TODO The virials are off by 1e-6, leading to
# pressure differences of 1e-3.
# I can't figure out why, but since PE and forces are
# matching exactly, I'll leave the tol
# set that high.
model_dir = build_examples.lj_graph(9 - 1)
with hoomd.htf.tfcompute(model_dir) as tfcompute:
hoomd.context.initialize()
N = 3 * 3
NN = N - 1
rcut = 5.0
system = hoomd.init.create_lattice(
unitcell=hoomd.lattice.sq(a=4.0), n=[3, 3])
nlist = hoomd.md.nlist.cell(check_period=1)
hoomd.md.integrate.mode_standard(dt=0.005)
hoomd.md.integrate.nvt(group=hoomd.group.all(), kT=1,
tau=0.2).randomize_velocities(seed=1)
tfcompute.attach(nlist, r_cut=rcut)
log = hoomd.analyze.log(
filename=None,
quantities=['potential_energy', 'pressure'],
period=1)
thermo_scalars = []
tf_virial = []
for i in range(5):
hoomd.run(3)
snapshot = system.take_snapshot()
tf_virial.append(tfcompute.get_virial_array())
thermo_scalars.append(
[log.query('potential_energy'),
log.query('pressure')])
# now run with stock lj
hoomd.context.initialize()
system = hoomd.init.create_lattice(unitcell=hoomd.lattice.sq(a=4.0),
n=[3, 3])
nlist = hoomd.md.nlist.cell(check_period=1)
hoomd.md.integrate.mode_standard(dt=0.005)
hoomd.md.integrate.nvt(group=hoomd.group.all(), kT=1,
tau=0.2).randomize_velocities(seed=1)
lj = hoomd.md.pair.lj(r_cut=5.0, nlist=nlist)
lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
log = hoomd.analyze.log(filename=None,
quantities=['potential_energy', 'pressure'],
period=1)
for i in range(5):
hoomd.run(3)
snapshot = system.take_snapshot()
v = snapshot.particles.velocity
lj_virial = np.array([lj.forces[j].virial for j in range(N)])
for j in range(N):
np.testing.assert_allclose(lj_virial[j][0:2],
tf_virial[i][j][0:2],
atol=1e-5)
def test_lj_forces(self):
N = 3 * 3
model_dir = build_examples.lj_graph(N - 1, self.tmp)
with hoomd.htf.tfcompute(model_dir) as tfcompute:
hoomd.context.initialize()
T = 10
rcut = 5.0
system = hoomd.init.create_lattice(
unitcell=hoomd.lattice.sq(a=4.0),
n=[3, 3])
nlist = hoomd.md.nlist.cell(check_period=1)
hoomd.md.integrate.mode_standard(dt=0.005)
hoomd.md.integrate.nvt(group=hoomd.group.all(),
kT=1, tau=0.2
).randomize_velocities(seed=1)
tfcompute.attach(nlist, r_cut=rcut)
hoomd.run(2)
tf_forces = []
for i in range(T):
hoomd.run(1)
snapshot = system.take_snapshot()
tf_forces.append([system.particles[j].net_force
for j in range(N)])
tf_forces = np.array(tf_forces)
# now run with stock lj
hoomd.context.initialize()
system = hoomd.init.create_lattice(
unitcell=hoomd.lattice.sq(a=4.0),
n=[3, 3])
nlist = hoomd.md.nlist.cell(check_period=1)
hoomd.md.integrate.mode_standard(dt=0.005)
hoomd.md.integrate.nvt(group=hoomd.group.all(), kT=1, tau=0.2
).randomize_velocities(seed=1)
lj = hoomd.md.pair.lj(r_cut=5.0, nlist=nlist)
lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
hoomd.run(2)
lj_forces = []
for i in range(T):
hoomd.run(1)
snapshot = system.take_snapshot()
lj_forces.append([system.particles[j].net_force for j in range(N)])
lj_forces = np.array(lj_forces)
for i in range(T):
for j in range(N):
np.testing.assert_allclose(tf_forces[i, j],
lj_forces[i, j], atol=1e-5)
def run_tf_lj(N, T):
model_dir = build_examples.lj_graph(N - 1)
with hoomd.htf.tfcompute(model_dir, _mock_mode=False) as tfcompute:
rcut = 5.0
system = init.create_lattice(
unitcell=hoomd.lattice.sq(a=4.0),
n=[np.sqrt(N).astype(np.int),
np.sqrt(N).astype(np.int)])
nlist = md.nlist.cell()
md.integrate.mode_standard(dt=0.005)
md.integrate.nvt(group=hoomd.group.all(), kT=1,
tau=0.2).randomize_velocities(seed=1)
tfcompute.attach(nlist, r_cut=rcut)
hoomd.run(2)
tf_forces = []
for i in range(T):
hoomd.run(1)
snapshot = system.take_snapshot()
tf_forces.append([system.particles[j].net_force for j in range(N)])
tf_forces = np.array(tf_forces)
return tf_forces
def test_overflow(self):
'''Use too small neighbor list and ensure error is thrown
TODO: It works, but the tfmanager thread early exit causes main thread to hang
'''
N = 8 * 8
model_dir = build_examples.lj_graph(4, self.tmp, check_nlist=True)
with hoomd.htf.tfcompute(model_dir) as tfcompute:
hoomd.context.initialize()
T = 10
rcut = 10.0
system = hoomd.init.create_lattice(
unitcell=hoomd.lattice.sq(a=4.0),
n=[8, 8])
nlist = hoomd.md.nlist.cell(check_period=1)
hoomd.md.integrate.mode_standard(dt=0.005)
hoomd.md.integrate.nvt(group=hoomd.group.all(),
kT=1, tau=0.2
).randomize_velocities(seed=1)
tfcompute.attach(nlist, r_cut=rcut)
with self.assertRaises(tf.errors.InvalidArgumentError):
hoomd.run(2)
def test_nlist_count(self):
'''Make sure nlist is full, not half
'''
model_dir = build_examples.lj_graph(9 - 1, self.tmp)
with hoomd.htf.tfcompute(model_dir) as tfcompute:
hoomd.context.initialize()
N = 3 * 3
NN = N - 1
T = 10
rcut = 5.0
system = hoomd.init.create_lattice(
unitcell=hoomd.lattice.sq(a=4.0),
n=[3, 3])
nlist = hoomd.md.nlist.cell()
hoomd.md.integrate.mode_standard(dt=0.001)
hoomd.md.integrate.nve(group=hoomd.group.all(
)).randomize_velocities(seed=1, kT=0.8)
tfcompute.attach(nlist, r_cut=rcut)
hoomd.run(1) # in lattice, should have 4 neighbors
nl = tfcompute.get_nlist_array()
ncount = np.sum(np.sum(nl**2, axis=2) > 0.1, axis=1)
self.assertEqual(np.min(ncount), 4)
