def test_dump_mols(crystal_params, equil_type):
"""Ensure the equilibration is close to initialisation."""
# Initialisation of snapshot
snap_init = init_from_crystal(crystal_params)
snap_init_mols = get_num_mols(snap_init)
# Equilibration
snap_equil = equilibrate(snap_init, crystal_params, equil_type)
snap_equil_mols = get_num_mols(snap_equil)
snap_out = init_from_file(crystal_params.outfile, crystal_params.molecule,
crystal_params.hoomd_args)
snap_out_mols = get_num_mols(snap_out)
assert snap_init_mols == snap_equil_mols
assert snap_init_mols == snap_out_mols
def test_thermalise(snapshot_from_none):
sim_params = snapshot_from_none["sim_params"]
snapshot = snapshot_from_none["snapshot"]
thermal_snap = thermalise(snapshot, sim_params)
num_mols = get_num_mols(thermal_snap)
mass = sim_params.molecule.mass
computed_trans_ke = (0.5 * mass * np.sum(
np.square(thermal_snap.particles.velocity[:num_mols]))) / num_mols
thermodynamic_ke = sim_params.molecule.dimensions * 0.5 * sim_params.temperature
assert np.isclose(computed_trans_ke, thermodynamic_ke, rtol=0.2)
def test_randomise_seed_different(snapshot_params):
num_mols = get_num_mols(snapshot_params["snapshot"])
snap1 = randomise_momenta(**snapshot_params, random_seed=0)
snap2 = randomise_momenta(**snapshot_params, random_seed=1)
angmom_similarity = np.sum(
np.square(snap1.particles.angmom[:num_mols] -
snap2.particles.angmom[:num_mols]),
axis=1,
)
velocity_similarity = np.sum(
np.square(snap1.particles.velocity[:num_mols] -
snap2.particles.velocity[:num_mols]),
axis=1,
)
if np.any(snapshot_params["sim_params"].molecule.moment_inertia != 0):
assert np.all(angmom_similarity > 0)
assert np.all(velocity_similarity > 0)
def test_moment_inertia(mol_params, scaling_factor):
"""Ensure moment of inertia is set correctly in setup."""
init_mol = np.array(mol_params.molecule.moment_inertia)
logger.debug("Moment Inertia before scaling: %s", init_mol)
init_mol *= scaling_factor
logger.debug("Moment Inertia after scaling: %s", init_mol)
with mol_params.temp_context(moment_inertia_scale=scaling_factor):
snapshot = init_from_none(mol_params)
context = hoomd.context.initialize(mol_params.hoomd_args)
snapshot = initialise_snapshot(snapshot, context,
mol_params).take_snapshot()
num_mols = get_num_mols(snapshot)
logger.debug("Simulation Moment Inertia: %s",
snapshot.particles.moment_inertia[0])
logger.debug("Intended Moment Inertia: %s", init_mol)
diff = snapshot.particles.moment_inertia[:num_mols] - init_mol
assert_allclose(diff, 0, atol=1e-1)
def test_randomise_iteration_id(snapshot_params, seed):
snap1 = randomise_momenta(**snapshot_params)
with snapshot_params["sim_params"].temp_context(iteration_id=seed):
snap2 = randomise_momenta(**snapshot_params)
num_mols = get_num_mols(snapshot_params["snapshot"])
angmom_similarity = np.sum(
np.square(snap1.particles.angmom[:num_mols] -
snap2.particles.angmom[:num_mols]),
axis=1,
)
velocity_similarity = np.sum(
np.square(snap1.particles.velocity[:num_mols] -
snap2.particles.velocity[:num_mols]),
axis=1,
)
if np.any(snapshot_params["sim_params"].molecule.moment_inertia != 0):
print("Molecule: ", snapshot_params["sim_params"].molecule)
assert np.all(angmom_similarity > 0)
assert np.all(velocity_similarity > 0)
def test_initialise_randomise(mol_params):
snapshot = hoomd.data.gsd_snapshot("test/data/Trimer-13.50-3.00.gsd")
context = hoomd.context.initialize(mol_params.hoomd_args)
num_mols = get_num_mols(snapshot)
with mol_params.temp_context(iteration_id=1):
sys = initialise_snapshot(snapshot, context, mol_params)
assert isinstance(sys, hoomd.data.system_data)
snap = sys.take_snapshot()
angmom_similarity = np.sum(
np.square(snap.particles.angmom[:num_mols] -
snapshot.particles.angmom[:num_mols]),
axis=1,
)
velocity_similarity = np.sum(
np.square(snap.particles.velocity[:num_mols] -
snapshot.particles.velocity[:num_mols]),
axis=1,
)
if np.any(mol_params.molecule.moment_inertia != 0):
assert np.all(angmom_similarity > 0)
assert np.all(velocity_similarity > 0)
def test_init_from_file(snapshot_params):
sim_params = snapshot_params["sim_params"]
snapshot = snapshot_params["snapshot"]
filename = sim_params.output / "testfile.gsd"
num_mols = get_num_mols(snapshot)
context = hoomd.context.initialize(args=sim_params.hoomd_args)
initialise_snapshot(snapshot, context, sim_params)
with context:
if sim_params.molecule.rigid:
group = hoomd.group.rigid_center()
else:
group = hoomd.group.all()
dump_frame(group, filename)
snap_file = init_from_file(filename, sim_params.molecule,
sim_params.hoomd_args)
assert snap_file.particles.types == sim_params.molecule.get_types()
assert snap_file.particles.N == snapshot.particles.N
assert np.all(
snap_file.particles.mass[:num_mols] == sim_params.molecule.mass)
assert_allclose(snap_file.particles.position[:num_mols],
snapshot.particles.position[:num_mols])
def test_init_crystal_position(crystal_params):
if isinstance(crystal_params.crystal, (TrimerP2)):
return
with crystal_params.temp_context(cell_dimensions=1):
snap = init_from_crystal(crystal_params,
equilibration=False,
minimize=False)
crys = crystal_params.crystal
num_mols = get_num_mols(snap)
mol_positions = crystal_params.molecule.get_relative_positions()
positions = np.concatenate([
pos + rowan.rotate(orient, mol_positions)
for pos, orient in zip(crys.positions, crys.get_orientations())
])
box = np.array([snap.box.Lx, snap.box.Ly, snap.box.Lz])
if crys.molecule.rigid:
sim_pos = snap.particles.position[num_mols:] % box
else:
sim_pos = snap.particles.position % box
init_pos = positions % box
assert_allclose(sim_pos, init_pos)
def test_molecule_masses(snapshot_from_none):
snap = snapshot_from_none["snapshot"]
molecule = snapshot_from_none["sim_params"].molecule
num_mols = get_num_mols(snap)
assert np.all(snap.particles.mass[:num_mols] == molecule.mass)
def num_mols(self):
return get_num_mols(self.snapshot)