def test_ron(simulation_factory, two_particle_snapshot_factory):
lj = md.pair.LJ(nlist=md.nlist.Cell(buffer=0.4),
mode='xplor',
default_r_cut=2.5)
lj.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
with pytest.raises(TypeConversionError):
lj.r_on[('A', 'A')] = 'str'
with pytest.raises(TypeConversionError):
lj.r_on[('A', 'A')] = [1, 2, 3]
sim = simulation_factory(two_particle_snapshot_factory(dimensions=3, d=.5))
integrator = md.Integrator(dt=0.005)
integrator.forces.append(lj)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
assert lj.r_on.to_base() == {}
lj.r_on[('A', 'A')] = 1.5
assert _equivalent_data_structures({('A', 'A'): 1.5}, lj.r_on.to_base())
sim.run(0)
assert _equivalent_data_structures({('A', 'A'): 1.5}, lj.r_on.to_base())
lj.r_on[('A', 'A')] = 1.0
assert _equivalent_data_structures({('A', 'A'): 1.0}, lj.r_on.to_base())
def simulation(simulation_factory, two_particle_snapshot_factory):
sim = simulation_factory(two_particle_snapshot_factory())
integrator = md.Integrator(0.005)
integrator.methods.append(md.methods.NVE(hoomd.filter.All()))
sim.operations += integrator
sim.state.thermalize_particle_momenta(hoomd.filter.All(), kT=1.0)
return sim
def test_running_simulation(simulation_factory, two_particle_snapshot_factory,
valid_body_definition):
rigid = md.constrain.Rigid()
rigid.body["A"] = valid_body_definition
langevin = md.methods.Langevin(kT=2.0, filter=hoomd.filter.Rigid())
lj = hoomd.md.pair.LJ(nlist=md.nlist.Cell(buffer=0.4), mode="shift")
lj.params.default = {"epsilon": 0.0, "sigma": 1}
lj.params[("A", "A")] = {"epsilon": 1.0}
lj.params[("B", "B")] = {"epsilon": 1.0}
lj.r_cut.default = 2**(1.0 / 6.0)
integrator = md.Integrator(dt=0.005, methods=[langevin], forces=[lj])
integrator.rigid = rigid
initial_snapshot = two_particle_snapshot_factory()
if initial_snapshot.communicator.rank == 0:
initial_snapshot.particles.types = ["A", "B"]
sim = simulation_factory(initial_snapshot)
sim.seed = 5
rigid.create_bodies(sim.state)
sim.operations += integrator
sim.run(5)
snapshot = sim.state.get_snapshot()
if sim.device.communicator.rank == 0:
check_bodies(snapshot, valid_body_definition)
def test_setting_body_after_attaching(simulation_factory,
two_particle_snapshot_factory,
valid_body_definition):
"""Test updating body definition without updating sim particles fails."""
rigid = md.constrain.Rigid()
langevin = md.methods.Langevin(kT=2.0, filter=hoomd.filter.Rigid())
lj = hoomd.md.pair.LJ(nlist=md.nlist.Cell(buffer=0.4), mode="shift")
lj.params.default = {"epsilon": 0.0, "sigma": 1}
lj.params[("A", "A")] = {"epsilon": 1.0}
lj.params[("B", "B")] = {"epsilon": 1.0}
lj.r_cut.default = 2**(1.0 / 6.0)
integrator = md.Integrator(dt=0.005, methods=[langevin], forces=[lj])
integrator.rigid = rigid
initial_snapshot = two_particle_snapshot_factory()
if initial_snapshot.communicator.rank == 0:
initial_snapshot.particles.types = ["A", "B"]
sim = simulation_factory(initial_snapshot)
sim.seed = 5
sim.operations += integrator
sim.run(1)
rigid.body["A"] = valid_body_definition
# This should error because the bodies have not been updated, but the
# setting should be fine.
with pytest.raises(RuntimeError):
sim.run(1)
def test_force_energy_accuracy(simulation_factory,
two_particle_snapshot_factory,
forces_and_energies):
pot = forces_and_energies.pair_potential(**forces_and_energies.extra_args,
nlist=md.nlist.Cell(),
r_cut=2.5, mode='none')
pot.params[('A', 'A')] = forces_and_energies.pair_potential_params
snap = two_particle_snapshot_factory(particle_types=['A'], d=0.75)
_update_snap(forces_and_energies.pair_potential, snap)
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(pot)
integrator.methods.append(md.methods.Langevin(hoomd.filter.All(),
kT=1, seed=1))
sim.operations.integrator = integrator
sim.run(0)
particle_distances = [0.75, 1.5]
for i in range(len(particle_distances)):
d = particle_distances[i]
r = np.array([0, 0, d]) / d
snap = sim.state.snapshot
if snap.exists:
snap.particles.position[0] = [0, 0, .1]
snap.particles.position[1] = [0, 0, d + .1]
sim.state.snapshot = snap
sim_energies = sim.operations.integrator.forces[0].energies
sim_forces = sim.operations.integrator.forces[0].forces
if sim_energies is not None:
assert isclose(sum(sim_energies), forces_and_energies.energies[i])
assert isclose(sim_forces[0], forces_and_energies.forces[i] * r)
assert isclose(sim_forces[0], -forces_and_energies.forces[i] * r)
def test_run(simulation_factory, lattice_snapshot_factory, valid_params):
pair_keys = valid_params.pair_potential_params.keys()
particle_types = list(set(itertools.chain.from_iterable(pair_keys)))
pot = valid_params.pair_potential(**valid_params.extra_args,
nlist=md.nlist.Cell(),
r_cut=2.5, mode='none')
pot.params = valid_params.pair_potential_params
snap = lattice_snapshot_factory(particle_types=particle_types,
n=7, a=1.7, r=0.01)
if snap.exists:
snap.particles.typeid[:] = np.random.randint(0,
len(snap.particles.types),
snap.particles.N)
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(pot)
integrator.methods.append(md.methods.Langevin(hoomd.filter.All(),
kT=1, seed=1))
sim.operations.integrator = integrator
sim.run(0)
for nsteps in [3, 5, 10]:
old_snap = sim.state.snapshot
sim.run(nsteps)
new_snap = sim.state.snapshot
if new_snap.exists:
assert not np.allclose(new_snap.particles.position,
old_snap.particles.position)
def test_custom_filter(make_filter_snapshot, simulation_factory):
"""Tests that custom particle filters work on simulations.
Specifically we test that using the Langevin integrator method, that only
particles selected by the custom filter move. Since the Langevin method uses
random movements we don't need to initialize velocities or have any forces
to test this.
"""
class NegativeCharge(CustomFilter):
"""Grab all particles with a negative charge."""
def __call__(self, state):
with state.cpu_local_snapshot as snap:
return snap.particles.tag[snap.particles.charge < 0]
def __hash__(self):
return hash(self.__class__.__name__)
def __eq__(self, other):
return isinstance(other, self.__class__)
charge_filter = NegativeCharge()
sim = simulation_factory(make_filter_snapshot())
# grabs tags on individual MPI ranks
with sim.state.cpu_local_snapshot as snap:
# Grab half of all particles on an MPI rank, 1 particle, or no particles
# depending on how many particles are local to the MPI ranks.
local_Np = snap.particles.charge.shape[0]
N_negative_charge = max(0, max(1, int(local_Np * 0.5)))
negative_charge_ind = np.random.choice(local_Np,
N_negative_charge,
replace=False)
# Get the expected tags returned by the custom filter and the positions
# that should vary and remain static for testing after running.
snap.particles.charge[negative_charge_ind] = -1.0
expected_tags = snap.particles.tag[negative_charge_ind]
positive_charge_tags = snap.particles.tag[snap.particles.charge > 0]
positive_charge_ind = snap.particles.rtag[positive_charge_tags]
original_positions = snap.particles.position[negative_charge_ind]
static_positions = snap.particles.position[positive_charge_ind]
# Test that the filter merely works as expected and that tags are correctly
# grabbed on local MPI ranks
assert all(np.sort(charge_filter(sim.state)) == np.sort(expected_tags))
# Test that the filter works when used in a simulation
langevin = md.methods.Langevin(charge_filter, 1.0)
sim.operations += md.Integrator(0.005, methods=[langevin])
sim.run(100)
snap = sim.state.snapshot
if snap.communicator.rank == 0:
assert not np.allclose(snap.particles.position[negative_charge_ind],
original_positions)
assert np.allclose(snap.particles.position[positive_charge_tags],
static_positions)
def make_sim(force_obj, snapshot=None, domain_decomposition=None):
sim = simulation_factory(snapshot, domain_decomposition)
npt = md.methods.NPT(hoomd.filter.All(),
kT=1,
tau=1,
S=1,
tauS=1,
couple="none")
integrator = md.Integrator(dt=0.005, forces=[force_obj], methods=[npt])
sim.operations.integrator = integrator
return sim
def test_mode(simulation_factory, two_particle_snapshot_factory, mode):
cell = md.nlist.Cell()
lj = md.pair.LJ(nlist=cell, r_cut=2.5, mode=mode)
lj.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
snap = two_particle_snapshot_factory(dimensions=3, d=.5)
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(lj)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
sim.run(1)
def test_error_on_invalid_body(simulation_factory,
two_particle_snapshot_factory,
valid_body_definition):
rigid = md.constrain.Rigid()
rigid.body["A"] = valid_body_definition
langevin = md.methods.Langevin(kT=2.0, filter=hoomd.filter.Rigid())
integrator = md.Integrator(dt=0.005, methods=[langevin])
integrator.rigid = rigid
initial_snapshot = two_particle_snapshot_factory()
if initial_snapshot.communicator.rank == 0:
initial_snapshot.particles.types = ["A", "B"]
sim = simulation_factory(initial_snapshot)
sim.operations += integrator
with pytest.raises(RuntimeError):
sim.run(0)
def test_failure_with_cpu_device_and_gpu_buffer():
"""Assert we cannot access gpu buffers with a cpu_device."""
device = hoomd.device.CPU()
snap = _make_two_particle_snapshot(device)
sim = hoomd.Simulation(device)
sim.create_state_from_snapshot(snap)
custom_force = MyForce('gpu_local_force_arrays')
npt = md.methods.NPT(hoomd.filter.All(),
kT=1,
tau=1,
S=1,
tauS=1,
couple="none")
integrator = md.Integrator(dt=0.005, forces=[custom_force], methods=[npt])
sim.operations.integrator = integrator
with pytest.raises(RuntimeError):
sim.run(1)
def test_force_energy_relationship(simulation_factory,
two_particle_snapshot_factory,
valid_params):
# don't really test DPD and DPDLJ for this test
pot_name = valid_params.pair_potential.__name__
if any(pot_name == name for name in ["DPD", "DPDLJ"]):
pytest.skip("Cannot test force energy relationship for " + pot_name +
" pair force")
pair_keys = valid_params.pair_potential_params.keys()
particle_types = list(set(itertools.chain.from_iterable(pair_keys)))
pot = valid_params.pair_potential(**valid_params.extra_args,
nlist=md.nlist.Cell(buffer=0.4),
default_r_cut=2.5)
for pair in valid_params.pair_potential_params:
pot.params[pair] = valid_params.pair_potential_params[pair]
if pot_name == 'DLVO':
pot.r_cut[pair] = 2.5 - ((0.2 + 0.5) / 2 - 1)
snap = two_particle_snapshot_factory(particle_types=particle_types, d=1.5)
_update_snap(valid_params.pair_potential, snap)
sim = simulation_factory(snap)
_skip_if_triplet_gpu_mpi(sim, valid_params.pair_potential)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(pot)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
sim.run(0)
for pair in valid_params.pair_potential_params:
snap = sim.state.get_snapshot()
if snap.communicator.rank == 0:
snap.particles.typeid[0] = particle_types.index(pair[0])
snap.particles.typeid[1] = particle_types.index(pair[1])
sim.state.set_snapshot(snap)
calculated_forces = _calculate_force(sim)
sim_forces = sim.operations.integrator.forces[0].forces
if sim_forces is not None:
np.testing.assert_allclose(calculated_forces[0],
sim_forces[0],
rtol=1e-05)
np.testing.assert_allclose(calculated_forces[1],
sim_forces[1],
rtol=1e-05)
def test_force_energy_relationship(simulation_factory,
two_particle_snapshot_factory,
valid_params):
# don't really test DPD and DPDLJ for this test
pot_name = valid_params.pair_potential.__name__
if any(pot_name == name for name in ["DPD", "DPDLJ"]):
pytest.skip("Cannot test force energy relationship for "
+ pot_name + " pair force")
pair_keys = valid_params.pair_potential_params.keys()
particle_types = list(set(itertools.chain.from_iterable(pair_keys)))
pot = valid_params.pair_potential(**valid_params.extra_args,
nlist=md.nlist.Cell(),
r_cut=2.5, mode='none')
for pair in valid_params.pair_potential_params:
pot.params[pair] = valid_params.pair_potential_params[pair]
snap = two_particle_snapshot_factory(particle_types=particle_types, d=1.5)
_update_snap(valid_params.pair_potential, snap)
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(pot)
integrator.methods.append(md.methods.Langevin(hoomd.filter.All(),
kT=1, seed=1))
sim.operations.integrator = integrator
sim.run(0)
for pair in valid_params.pair_potential_params:
snap = sim.state.snapshot
if snap.exists:
snap.particles.typeid[0] = particle_types.index(pair[0])
snap.particles.typeid[1] = particle_types.index(pair[1])
sim.state.snapshot = snap
calculated_forces = _calculate_force(sim)
sim_forces = sim.operations.integrator.forces[0].forces
if sim_forces is not None:
np.testing.assert_allclose(calculated_forces[0],
sim_forces[0],
rtol=1e-06)
np.testing.assert_allclose(calculated_forces[1],
sim_forces[1],
rtol=1e-06)
def test_run(simulation_factory, lattice_snapshot_factory, pair_potential):
snap = lattice_snapshot_factory(particle_types=['A', 'B'],
n=7, a=1.7, r=0.01)
if snap.exists:
snap.particles.typeid[:] = np.random.randint(0,
len(snap.particles.types),
snap.particles.N)
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(pair_potential)
integrator.methods.append(md.methods.Langevin(hoomd.filter.All(),
kT=1))
sim.operations.integrator = integrator
for nsteps in [3, 5, 10]:
old_snap = sim.state.snapshot
sim.run(nsteps)
new_snap = sim.state.snapshot
if new_snap.exists:
assert not np.allclose(new_snap.particles.position,
old_snap.particles.position)
def test_running_without_body_definition(simulation_factory,
two_particle_snapshot_factory):
rigid = md.constrain.Rigid()
langevin = md.methods.Langevin(kT=2.0, filter=hoomd.filter.Rigid())
lj = hoomd.md.pair.LJ(nlist=md.nlist.Cell(), mode="shift")
lj.params.default = {"epsilon": 0.0, "sigma": 1}
lj.params[("A", "A")] = {"epsilon": 1.0}
lj.params[("B", "B")] = {"epsilon": 1.0}
lj.r_cut.default = 2**(1.0 / 6.0)
integrator = md.Integrator(dt=0.005, methods=[langevin], forces=[lj])
integrator.rigid = rigid
initial_snapshot = two_particle_snapshot_factory()
if initial_snapshot.communicator.rank == 0:
initial_snapshot.particles.types = ["A", "B"]
sim = simulation_factory(initial_snapshot)
sim.seed = 5
sim.operations += integrator
sim.run(1)
def test_data_buffers_readonly(local_force_names,
two_particle_snapshot_factory,
simulation_factory):
"""Ensure local data buffers for non-custom force classes are read-only."""
nlist = md.nlist.Cell(buffer=0.2)
lj = md.pair.LJ(nlist, default_r_cut=2.0)
lj.params[('A', 'A')] = dict(epsilon=1.0, sigma=1.0)
snap = two_particle_snapshot_factory()
sim = simulation_factory(snap)
langevin = md.methods.Langevin(hoomd.filter.All(), kT=1)
integrator = md.Integrator(dt=0.005, forces=[lj], methods=[langevin])
sim.operations.integrator = integrator
sim.run(2)
for local_force_name in local_force_names:
with getattr(lj, local_force_name) as arrays:
if not _gpu_device_and_no_cupy(sim):
_assert_buffers_readonly(arrays)
def test_rcut(simulation_factory, two_particle_snapshot_factory):
lj = md.pair.LJ(nlist=md.nlist.Cell(), r_cut=2.5)
assert lj.r_cut.default == 2.5
lj.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
with pytest.raises(hoomd.data.typeconverter.TypeConversionError):
lj.r_cut[('A', 'A')] = 'str'
with pytest.raises(hoomd.data.typeconverter.TypeConversionError):
lj.r_cut[('A', 'A')] = [1, 2, 3]
sim = simulation_factory(two_particle_snapshot_factory(dimensions=3, d=.5))
integrator = md.Integrator(dt=0.005)
integrator.forces.append(lj)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
lj.r_cut[('A', 'A')] = 2.5
assert _equivalent_data_structures({('A', 'A'): 2.5}, lj.r_cut.to_dict())
sim.run(0)
assert _equivalent_data_structures({('A', 'A'): 2.5}, lj.r_cut.to_dict())
def test_shift_mode_with_lrc(simulation_factory, two_particle_snapshot_factory,
mode):
cell = md.nlist.Cell(buffer=0.4)
lj = md.pair.LJ(nlist=cell,
default_r_cut=2.5,
mode=mode,
tail_correction=True)
lj.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
snap = two_particle_snapshot_factory(dimensions=3, d=.5)
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(lj)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
shift_allowed_modes = {'none'}
if mode not in shift_allowed_modes:
with pytest.raises(RuntimeError):
sim.run(1)
else:
sim.run(1)
def test_attaching(simulation_factory, two_particle_snapshot_factory,
valid_body_definition):
rigid = md.constrain.Rigid()
rigid.body["A"] = valid_body_definition
langevin = md.methods.Langevin(kT=2.0, filter=hoomd.filter.Rigid())
integrator = md.Integrator(dt=0.005, methods=[langevin])
integrator.rigid = rigid
initial_snapshot = two_particle_snapshot_factory()
if initial_snapshot.communicator.rank == 0:
initial_snapshot.particles.types = ["A", "B"]
sim = simulation_factory(initial_snapshot)
rigid.create_bodies(sim.state)
sim.operations += integrator
sim.run(0)
for key, value in rigid.body["A"].items():
if (isinstance(value, Sequence) and len(value) > 0
and not isinstance(value[0], str)):
assert np.allclose(value, valid_body_definition[key])
else:
assert value == valid_body_definition[key]
def test_run(simulation_factory, lattice_snapshot_factory, pair_potential):
snap = lattice_snapshot_factory(particle_types=['A', 'B'],
n=7,
a=2.0,
r=0.01)
if snap.communicator.rank == 0:
snap.particles.typeid[:] = np.random.randint(0,
len(snap.particles.types),
snap.particles.N)
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005, integrate_rotational_dof=True)
integrator.forces.append(pair_potential)
integrator.methods.append(md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
old_snap = sim.state.get_snapshot()
sim.run(5)
new_snap = sim.state.get_snapshot()
forces = pair_potential.forces
energies = pair_potential.energies
if new_snap.communicator.rank == 0:
assert not np.allclose(new_snap.particles.position,
old_snap.particles.position)
assert np.any(energies != 0)
assert np.any(forces != 0)
def test_force_energy_accuracy(simulation_factory,
two_particle_snapshot_factory,
forces_and_energies):
pot_name = forces_and_energies.pair_potential.__name__
if pot_name == "DPD" or pot_name == "DPDLJ":
pytest.skip("Cannot test force energy accuracy for " + pot_name +
" pair force")
pot = forces_and_energies.pair_potential(**forces_and_energies.extra_args,
nlist=md.nlist.Cell(),
default_r_cut=2.5)
pot.params[('A', 'A')] = forces_and_energies.pair_potential_params
snap = two_particle_snapshot_factory(particle_types=['A'], d=0.75)
_update_snap(forces_and_energies.pair_potential, snap)
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(pot)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
sim.run(0)
particle_distances = [0.75, 1.5]
for i in range(len(particle_distances)):
d = particle_distances[i]
r = np.array([0, 0, d]) / d
snap = sim.state.snapshot
if snap.communicator.rank == 0:
snap.particles.position[0] = [0, 0, .1]
snap.particles.position[1] = [0, 0, d + .1]
sim.state.snapshot = snap
sim_energies = sim.operations.integrator.forces[0].energies
sim_forces = sim.operations.integrator.forces[0].forces
if sim_energies is not None:
assert isclose(sum(sim_energies), forces_and_energies.energies[i])
assert isclose(sim_forces[0], forces_and_energies.forces[i] * r)
assert isclose(sim_forces[0], -forces_and_energies.forces[i] * r)
def test_attached_params(simulation_factory, lattice_snapshot_factory,
valid_params):
pair_potential, pair_potential_dict, extra_args = valid_params
pair_keys = valid_params.pair_potential_params.keys()
particle_types = list(set(itertools.chain.from_iterable(pair_keys)))
pot = valid_params.pair_potential(**valid_params.extra_args,
nlist=md.nlist.Cell(),
r_cut=2.5, mode='none')
pot.params = valid_params.pair_potential_params
snap = lattice_snapshot_factory(particle_types=particle_types,
n=10, a=1.5, r=0.01)
_update_snap(valid_params.pair_potential, snap)
if snap.exists:
snap.particles.typeid[:] = np.random.randint(0,
len(snap.particles.types),
snap.particles.N)
sim = simulation_factory(snap)
sim.operations.integrator = md.Integrator(dt=0.005)
sim.operations.integrator.forces.append(pot)
sim.run(1)
assert _equivalent_data_structures(valid_params.pair_potential_params,
pot.params.to_dict())
def test_tail_corrections(simulation_factory, two_particle_snapshot_factory):
# the tail correction should always decrease the potential energy with a LJ
# pair potential and the cutoff is greater than sigma
# further, the pressure correction should always be negative for the LJ
# potenial if r_cut is greater than 2^(1/6)sigma
sims = {}
sigma = 1.0
epsilon = 0.5
d_pair = 1.5
r_cut = 2.0
for tail_correction in [True, False]:
cell = md.nlist.Cell(buffer=0.4)
lj = md.pair.LJ(nlist=cell,
default_r_cut=r_cut,
mode='none',
tail_correction=tail_correction)
lj.params[('A', 'A')] = {'sigma': sigma, 'epsilon': epsilon}
snap = two_particle_snapshot_factory(dimensions=3, d=d_pair)
v1 = np.array([0.46168675, -0.21020661, 0.21240303])
v2 = -v1 # zero linear momentum
if snap.communicator.rank == 0:
snap.particles.velocity[0] = v1
snap.particles.velocity[1] = v2
sim = simulation_factory(snap)
integrator = md.Integrator(dt=0.005)
integrator.forces.append(lj)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
sim.always_compute_pressure = True
thermodynamic_properties = hoomd.md.compute.ThermodynamicQuantities(
filter=hoomd.filter.All())
sim.operations.computes.append(thermodynamic_properties)
sim.run(0)
sims[tail_correction] = sim
e_true = sims[True].operations.computes[0].potential_energy
e_false = sims[False].operations.computes[0].potential_energy
p_true = sims[True].operations.computes[0].pressure
p_false = sims[False].operations.computes[0].pressure
N = sim.state.N_particles
volume = sim.state.box.volume
rho = N / volume
def lj_energy(r, sig, eps):
return 4 * eps * ((sig / r)**12 - (sig / r)**6)
def energy_correction(sigma, epsilon, r_cut, rho, N):
"""Long-range tail correction to energy."""
lj1 = 4.0 * epsilon * sigma**12.0
lj2 = 4.0 * epsilon * sigma**6.0
integral = lj1 / 9 / r_cut**9 - lj2 / 3 / r_cut**3
return 2 * N * np.pi * rho * integral
def lj_force_mag(r, sig, eps):
"""Magnitude of force on particles from LJ potential a distance r."""
return 24 * eps / r * (2 * (sig / r)**12 - (sig / r)**6)
def pressure_correction(sigma, epsilon, r_cut, rho):
"""Long-range tail correction to pressure."""
lj1 = 4.0 * epsilon * sigma**12.0
lj2 = 4.0 * epsilon * sigma**6.0
integral = lj1 * 4 / 3 / r_cut**9 - lj2 * 2 / r_cut**3
return 4 / 6 * rho**2 * np.pi * integral
dE = energy_correction(sigma, epsilon, r_cut, rho, N)
mass = 1.0
ke = 0.5 * mass * (np.dot(v1, v1) + np.dot(v2, v2))
ljf = lj_force_mag(d_pair, sigma, epsilon)
mean_virial = 1 / 3 * ljf * d_pair
pressure_should_be = (2 * ke / 3 + mean_virial) / volume
dP = pressure_correction(sigma, epsilon, r_cut, rho)
# energy regression test
np.testing.assert_allclose(e_false, lj_energy(d_pair, sigma, epsilon))
np.testing.assert_allclose(e_true, lj_energy(d_pair, sigma, epsilon) + dE)
# pressure regression test
np.testing.assert_allclose(p_false, pressure_should_be)
np.testing.assert_allclose(p_true, pressure_should_be + dP)
# make sure corrections correct in the right direction
assert e_true < e_false
assert p_true < p_false
def make_langevin_integrator(force):
integrator = md.Integrator(dt=0.005, integrate_rotational_dof=True)
integrator.forces.append(force)
integrator.methods.append(md.methods.Langevin(hoomd.filter.All(), kT=1))
return integrator
def test_conservation(simulation_factory, lattice_snapshot_factory):
# For test, use a unit area hexagon.
particle_vertices = np.array([[6.20403239e-01, 0.00000000e+00, 0],
[3.10201620e-01, 5.37284966e-01, 0],
[-3.10201620e-01, 5.37284966e-01, 0],
[-6.20403239e-01, 7.59774841e-17, 0],
[-3.10201620e-01, -5.37284966e-01, 0],
[3.10201620e-01, -5.37284966e-01, 0]])
area = 1.0
circumcircle_radius = 0.6204032392788702
incircle_radius = 0.5372849659264116
num_vertices = len(particle_vertices)
circumcircle_diameter = 2 * circumcircle_radius
# Just initialize in a simple cubic lattice.
sim = simulation_factory(
lattice_snapshot_factory(a=4 * circumcircle_diameter,
n=10,
dimensions=2))
sim.seed = 175
# Initialize moments of inertia since original simulation was HPMC.
mass = area
# https://math.stackexchange.com/questions/2004798/moment-of-inertia-for-a-n-sided-regular-polygon # noqa
moment_inertia = (mass * circumcircle_diameter**2 / 6)
moment_inertia *= (1 + 2 * np.cos(np.pi / num_vertices)**2)
with sim.state.cpu_local_snapshot as snapshot:
snapshot.particles.mass[:] = mass
snapshot.particles.moment_inertia[:] = np.array([0, 0, moment_inertia])
# Not sure if this should be incircle or circumcircle;
# probably doesn't matter based on current usage, but may
# matter in the future for the potential if it's modified
# to actually use diameter.
snapshot.particles.diameter[:] = circumcircle_diameter
kT = 0.3
sim.state.thermalize_particle_momenta(hoomd.filter.All(), kT)
# Create box resize updater
packing_fraction = 0.4
final_area = area * sim.state.N_particles / packing_fraction
L_final = np.sqrt(final_area)
final_box = hoomd.Box.square(L_final)
n_compression_start = int(1e4)
n_compression_end = int(1e5)
n_compression_total = n_compression_end - n_compression_start
box_resize = hoomd.update.BoxResize(
box1=sim.state.box,
box2=final_box,
trigger=int(n_compression_total / 10000),
variant=hoomd.variant.Ramp(0, 1, n_compression_start,
n_compression_total),
filter=hoomd.filter.All())
sim.operations += box_resize
# Define forces and methods
r_cut_scale = 1.3
kernel_scale = (1 / np.cos(np.pi / num_vertices))
incircle_diameter = 2 * incircle_radius
r_cut_set = incircle_diameter * kernel_scale * r_cut_scale
alj = md.pair.aniso.ALJ(default_r_cut=r_cut_set, nlist=md.nlist.Cell(0.4))
alj.shape["A"] = {
"vertices": particle_vertices,
"faces": [],
"rounding_radii": 0
}
alpha = 0 # Make it WCA-only (no attraction)
eps_att = 1.0
alj.params[("A", "A")] = {
"epsilon": eps_att,
"sigma_i": incircle_diameter,
"sigma_j": incircle_diameter,
"alpha": alpha
}
nve = md.methods.NVE(filter=hoomd.filter.All())
integrator = md.Integrator(dt=1e-4,
forces=[alj],
methods=[nve],
integrate_rotational_dof=True)
sim.operations.integrator = integrator
# Compress box
sim.run(n_compression_end)
thermo = md.compute.ThermodynamicQuantities(hoomd.filter.All())
sim.operations += thermo
# Reset velocities after the compression, and equilibriate
sim.state.thermalize_particle_momenta(hoomd.filter.All(), kT)
sim.run(1000)
# run sim and get values back
w = hoomd.conftest.ManyListWriter([(thermo, 'potential_energy'),
(thermo, 'kinetic_energy'),
(integrator, 'linear_momentum')])
writer = hoomd.write.CustomWriter(action=w, trigger=1)
sim.operations.writers.append(writer)
sim.run(1000)
pe, ke, momentum = w.data
total_energies = np.array(pe) + np.array(ke)
# Ensure energy conservation up to the 3 digit per-particle.
npt.assert_allclose(total_energies,
total_energies[0],
atol=0.03 * sim.state.N_particles)
# Test momentum conservation.
p_magnitude = np.linalg.norm(momentum, axis=-1)
npt.assert_allclose(p_magnitude, p_magnitude[0], atol=1e-13)
def test_type_shapes(simulation_factory, two_particle_snapshot_factory):
alj = md.pair.aniso.ALJ(md.nlist.Cell(buffer=0.1))
sim = simulation_factory(two_particle_snapshot_factory(d=2.0))
sim.operations.integrator = md.Integrator(0.005, forces=[alj])
alj.r_cut.default = 2.5
octahedron = [(0.5, 0, 0), (-0.5, 0, 0), (0, 0.5, 0), (0, -0.5, 0),
(0, 0, 0.5), (0, 0, -0.5)]
faces = [[5, 3, 1], [0, 3, 5], [1, 3, 4], [4, 3, 0], [5, 2, 0], [1, 2, 5],
[0, 2, 4], [4, 2, 1]]
rounding_radius = 0.1
alj.shape["A"] = {
"vertices": octahedron,
"faces": faces,
"rounding_radii": rounding_radius
}
# We use a non-zero sigma_i to ensure that it is added appropriately to the
# rounding radius.
alj.params[("A", "A")] = {
"epsilon": 1.0,
"sigma_i": 0.1,
"sigma_j": 0.1,
"alpha": 1
}
with pytest.raises(hoomd.error.DataAccessError):
alj.type_shapes
def get_rounding_radius(base, param_spec):
modification = param_spec["sigma_i"] * param_spec["contact_ratio_i"]
return rounding_radius + modification / 2
sim.run(0)
shape_spec = alj.type_shapes
assert len(shape_spec) == 1
shape_spec = shape_spec[0]
assert shape_spec["type"] == "ConvexPolyhedron"
assert np.allclose(shape_spec["vertices"], octahedron)
assert np.isclose(
shape_spec["rounding_radius"],
get_rounding_radius(rounding_radius, alj.params[("A", "A")]))
ellipse_axes = (0.1, 0.2, 0.3)
alj.shape["A"] = {
"vertices": [],
"faces": [],
"rounding_radii": ellipse_axes
}
shape_spec = alj.type_shapes
assert len(shape_spec) == 1
shape_spec = shape_spec[0]
assert shape_spec["type"] == "Ellipsoid"
assert np.isclose(
shape_spec["a"],
get_rounding_radius(ellipse_axes[0], alj.params[("A", "A")]))
assert np.isclose(
shape_spec["a"],
get_rounding_radius(ellipse_axes[1], alj.params[("A", "A")]))
assert np.isclose(
shape_spec["a"],
get_rounding_radius(ellipse_axes[2], alj.params[("A", "A")]))
sim.operations.integrator.forces.remove(alj)
sim = simulation_factory(two_particle_snapshot_factory(dimensions=2, d=2))
sim.operations.integrator = md.Integrator(0.005, forces=[alj])
square = [(0.5, 0, 0), (-0.5, 0, 0), (-0.5, -0.5, 0), (0.5, 0.5, 0)]
alj.shape["A"] = {
"vertices": square,
"faces": [],
"rounding_radii": rounding_radius
}
sim.run(0)
shape_spec = alj.type_shapes
assert len(shape_spec) == 1
shape_spec = shape_spec[0]
assert shape_spec["type"] == "Polygon"
assert np.allclose(shape_spec["vertices"], np.array(square)[:, :2])
assert np.isclose(
shape_spec["rounding_radius"],
get_rounding_radius(rounding_radius, alj.params[("A", "A")]))
alj.shape["A"] = {
"vertices": [],
"faces": [],
"rounding_radii": ellipse_axes
}
shape_spec = alj.type_shapes
assert len(shape_spec) == 1
shape_spec = shape_spec[0]
assert shape_spec["type"] == "Ellipsoid"
assert np.isclose(
shape_spec["a"],
get_rounding_radius(ellipse_axes[0], alj.params[("A", "A")]))
assert np.isclose(
shape_spec["a"],
get_rounding_radius(ellipse_axes[1], alj.params[("A", "A")]))
def populate_sim(sim):
"""Add an integrator for the following tests."""
sim.operations.integrator = md.Integrator(
dt=0.005, methods=[md.methods.NVE(hoomd.filter.All())])
return sim
def test_energy_shifting(simulation_factory, two_particle_snapshot_factory):
# A subtle bug existed where we used "shifted" instead of "shift" in Python
# and in C++ we used else if clauses with no error raised if the set Python
# mode fell through. This means the actual shift mode was not set.
pytest.skip("Test is broken.")
def S_r(r, r_cut, r_on):
if r < r_on:
return 1
elif r > r_cut:
return 0
numerator = (
(r_cut**2 - r**2)**2) * (r_cut**2 + 2 * r**2 - 3 * r_on**2)
denominator = (r_cut**2 - r_on**2)**3
return numerator / denominator
r_cut = 2.5
r_on = 0.5
r = 1.0
lj = md.pair.LJ(nlist=md.nlist.Cell(), r_cut=r_cut)
lj.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
sim = simulation_factory(two_particle_snapshot_factory(dimensions=3, d=r))
integrator = md.Integrator(dt=0.005)
integrator.forces.append(lj)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
sim.run(0)
energies = sim.operations.integrator.forces[0].energies
if energies is not None:
E_r = sum(energies)
snap = sim.state.snapshot
if snap.exists:
snap.particles.position[0] = [0, 0, .1]
snap.particles.position[1] = [0, 0, r_cut + .1]
sim.state.snapshot = snap
energies = sim.operations.integrator.forces[0].energies
if energies is not None:
E_rcut = sum(energies)
lj_shift = md.pair.LJ(nlist=md.nlist.Cell(), mode='shift', r_cut=r_cut)
lj_shift.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
integrator = md.Integrator(dt=0.005)
integrator.forces.append(lj_shift)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
sim.run(0)
snap = sim.state.snapshot
if snap.exists:
snap.particles.position[0] = [0, 0, .1]
snap.particles.position[1] = [0, 0, r + .1]
sim.state.snapshot = snap
energies = sim.operations.integrator.forces[0].energies
if energies is not None:
assert sum(energies) == E_r - E_rcut
lj_xplor = md.pair.LJ(nlist=md.nlist.Cell(), mode='xplor', r_cut=r_cut)
lj_xplor.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
lj_xplor.r_on[('A', 'A')] = 0.5
integrator = md.Integrator(dt=0.005)
integrator.forces.append(lj_xplor)
integrator.methods.append(
hoomd.md.methods.Langevin(hoomd.filter.All(), kT=1))
sim.operations.integrator = integrator
sim.run(0)
energies = sim.operations.integrator.forces[0].energies
if energies is not None:
xplor_E = sum(energies)
assert xplor_E == E_r * S_r(r, r_cut, r_on)
lj_xplor.r_on[('A', 'A')] = 3.0
assert sum(energies) == E_r - E_rcut
def test_energy_shifting(simulation_factory, two_particle_snapshot_factory):
# A subtle bug existed where we used "shifted" instead of "shift" in Python
# and in C++ we used else if clauses with no error raised if the set Python
# mode fell through. This means the actual shift mode was not set.
def S_r(r, r_cut, r_on): # noqa: N802 - allow uppercase function name
if r < r_on:
return 1
elif r > r_cut:
return 0
numerator = (
(r_cut**2 - r**2)**2) * (r_cut**2 + 2 * r**2 - 3 * r_on**2)
denominator = (r_cut**2 - r_on**2)**3
return numerator / denominator
def set_distance(simulation, distance):
snap = sim.state.get_snapshot()
if snap.communicator.rank == 0:
snap.particles.position[0] = [0, 0, .1]
snap.particles.position[1] = [0, 0, distance + .1]
sim.state.set_snapshot(snap)
def get_energy(simulation):
energies = sim.operations.integrator.forces[0].energies
if energies is None:
return
return sum(energies)
r_cut = 2.5
distance = 1.1
lj = md.pair.LJ(nlist=md.nlist.Cell(buffer=0.4), default_r_cut=r_cut * 1.2)
lj.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
sim = simulation_factory(
two_particle_snapshot_factory(dimensions=3, d=distance))
integrator = md.Integrator(dt=0.005, forces=[lj])
sim.operations.integrator = integrator
sim.run(0)
E_r = get_energy(sim)
# Get energy at r_cut.
set_distance(sim, r_cut)
E_r_cut = get_energy(sim)
lj_shift = md.pair.LJ(nlist=md.nlist.Cell(buffer=0.4),
mode='shift',
default_r_cut=r_cut)
lj_shift.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
integrator.forces = [lj_shift]
set_distance(sim, distance)
energies = sim.operations.integrator.forces[0].energies
if energies is not None:
assert math.isclose(sum(energies), E_r - E_r_cut)
r_on = 0.5
lj_xplor = md.pair.LJ(nlist=md.nlist.Cell(buffer=0.4),
mode='xplor',
default_r_cut=r_cut)
lj_xplor.params[('A', 'A')] = {'sigma': 1, 'epsilon': 0.5}
lj_xplor.r_on[('A', 'A')] = r_on
integrator.forces = [lj_xplor]
# When 0 < r_on < r_ij < r_cut
energies = sim.operations.integrator.forces[0].energies
if energies is not None:
assert math.isclose(sum(energies), E_r * S_r(distance, r_cut, r_on))
# When 0 < r_ij < r_on < r_cut
lj_xplor.r_on[('A', 'A')] = distance * 1.2
sim.run(1) # recompute forces
energies = sim.operations.integrator.forces[0].energies
if energies is not None:
assert math.isclose(sum(energies), E_r)
# When 0 < r_ij < r_cut < r_on
lj_xplor.r_on[('A', 'A')] = r_cut * 1.2
sim.run(1) # recompute forces
energies = sim.operations.integrator.forces[0].energies
if energies is not None:
assert math.isclose(sum(energies), E_r - E_r_cut)
def make_langevin_integrator(force):
integrator = md.Integrator(dt=0.005)
integrator.forces.append(force)
integrator.methods.append(
md.methods.Langevin(hoomd.filter.All(), kT=1, seed=1))
return integrator