def test_lj_energy(self):
model = build_examples.LJModel(32)
tfcompute = htf.tfcompute(model)
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_force_output(self):
Ne = 5
c = hoomd.context.initialize('')
model = build_examples.LJModel(32, output_forces=False)
model.compile(loss='MeanSquaredError')
tfcompute = htf.tfcompute(model)
rcut = 3.0
system = hoomd.init.create_lattice(
unitcell=hoomd.lattice.sq(a=2.0),
n=[Ne, Ne])
c.sorter.disable()
nlist = hoomd.md.nlist.cell(check_period=1)
hoomd.md.integrate.mode_standard(dt=0.01)
lj = hoomd.md.pair.lj(r_cut=rcut, nlist=nlist)
lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)
lj2 = hoomd.md.pair.lj(r_cut=rcut, nlist=nlist)
lj2.pair_coeff.set('A', 'A', epsilon=4.0, sigma=0.8)
hoomd.md.integrate.nve(group=hoomd.group.all(
)).randomize_velocities(seed=1, kT=0.8)
tfcompute.attach(nlist, train=True, r_cut=rcut, period=100)
tfcompute.set_reference_forces(lj)
hoomd.run(300)
error = model.metrics[0].result().numpy()
assert abs(error) < 1e-5
# now check difference between particle forces and
# forces from htf
lj_forces = np.array([lj.forces[j].force for j in range(Ne**2)])
lj_energy = np.array([lj.forces[j].energy for j in range(Ne**2)])
np.testing.assert_allclose(tfcompute.get_forces_array(
)[:, :3], lj_forces)
np.testing.assert_allclose(tfcompute.get_forces_array(
)[:, 3], lj_energy)
def test_lj_forces(self):
model = build_examples.LJModel(32)
tfcompute = htf.tfcompute(model)
T = 10
N = 5 * 5
rcut = 5.0
system = hoomd.init.create_lattice(
unitcell=hoomd.lattice.sq(a=3.0),
n=[5, 5])
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(20)
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=3.0),
n=[5, 5])
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(20)
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)
# make sure we wrote test to have non-zero forces
assert np.sum(
lj_forces[i, j]**2) > 1e-4**2, 'Forces are too low to assess!'
def test_overflow(self):
'''Use too small neighbor list and ensure error is thrown
'''
N = 8 * 8
model = build_examples.LJModel(4, check_nlist=True)
tfcompute = htf.tfcompute(model)
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 run_tf_lj(N, T):
model = build_examples.LJModel(256)
tfcompute = hoomd.htf.tfcompute(model)
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_nlist_count(self):
'''Make sure nlist is full, not half
'''
model = build_examples.LJModel(32)
tfcompute = htf.tfcompute(model)
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)
def test_compute_pairwise(self):
model = build_examples.LJModel(4)
r = np.linspace(0.5, 1.5, 5)
output = hoomd.htf.compute_pairwise(model, r)
np.testing.assert_equal(output[0].shape[0], len(r),
'Pairwise not calculated correctly')