def test_orthorhombic_equil(crystal_params):
"""Ensure the equilibration is close to initialisation."""
snap_min = init_from_crystal(crystal_params)
snap_ortho = make_orthorhombic(snap_min)
snap_equil = equilibrate(snap_ortho, crystal_params, equil_type="crystal")
# Simulation box within 20% of initialisation
for attribute in ["Lx", "Ly", "Lz", "xy", "xz", "yz"]:
assert np.isclose(
getattr(snap_ortho.box, attribute),
getattr(snap_equil.box, attribute),
rtol=0.2,
)
def test_orthorhombic_sims(cell_dimensions, crystal_params):
"""Test the initialisation from a crystal unit cell.
This also ensures there is no unusual things going on with the calculation
of the orthorhombic unit cell.
"""
# Multiple of 6 works nicely with the p2 crystal
cell_dimensions = cell_dimensions * 6
with crystal_params.temp_context(cell_dimensions=cell_dimensions):
snapshot = init_from_crystal(crystal_params)
snapshot = equilibrate(snapshot, crystal_params, equil_type="crystal")
snapshot = make_orthorhombic(snapshot)
temp_context = hoomd.context.initialize(crystal_params.hoomd_args)
production(snapshot, temp_context, crystal_params, dynamics=False)
def test_minimize_snapshot(crystal_params, ensemble):
snap = init_from_crystal(crystal_params,
equilibration=False,
minimize=False)
min_snap = minimize_snapshot(snap, crystal_params, ensemble)
if ensemble == "NPH":
rtol = 0.2
else:
rtol = 0
assert_allclose(snap.box.Lx, min_snap.box.Lx, rtol=rtol)
assert_allclose(snap.box.Ly, min_snap.box.Ly, rtol=rtol)
assert_allclose(snap.box.Lz, min_snap.box.Lz, rtol=rtol)
assert_allclose(snap.box.xy, min_snap.box.xy, rtol=rtol)
assert_allclose(snap.box.xz, min_snap.box.xz, rtol=rtol)
assert_allclose(snap.box.yz, min_snap.box.yz, rtol=rtol)
def test_orthorhombic_init(crystal_params, cell_dimensions):
"""Ensure orthorhombic cell initialises correctly."""
snap = init_from_crystal(crystal_params)
snap_ortho = make_orthorhombic(snap)
assert np.all(snap_ortho.particles.position == snap.particles.position)
assert np.all(
snap_ortho.particles.position[:, 0] < snap_ortho.box.Lx / 2.0)
assert np.all(
snap_ortho.particles.position[:, 0] >= -snap_ortho.box.Lx / 2.0)
assert np.all(
snap_ortho.particles.position[:, 1] < snap_ortho.box.Ly / 2.0)
assert np.all(
snap_ortho.particles.position[:, 1] >= -snap_ortho.box.Ly / 2.0)
assert snap_ortho.box.xy == 0
assert snap_ortho.box.xz == 0
assert snap_ortho.box.yz == 0
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_init_crystal(crystal_params):
"""Test the initialisation of all crystals."""
snap = init_from_crystal(crystal_params)
Nx, Ny, _ = crystal_params.cell_dimensions
unitcell = crystal_params.crystal.cell_matrix
logger.debug("Unitcell: %s", unitcell)
Lx = np.linalg.norm(np.dot(unitcell, np.array([1, 0, 0])))
Ly = np.linalg.norm(np.dot(unitcell, np.array([0, 1, 0])))
assert Lx > 0
assert Ly > 0
assert Nx > 0
assert Ny > 0
# Simulation box within 20% of initialisation
assert_allclose(snap.box.Lx, Lx * Nx, rtol=0.2)
assert_allclose(snap.box.Ly, Ly * Ny, rtol=0.2)
def test_trimerPg_init_position():
sim_params = SimulationParams(crystal=TrimerPg(), cell_dimensions=1)
snap = init_from_crystal(sim_params, equilibration=False, minimize=False)
manual = np.array(
[
[-1.088_551_4, 1.025_773_4, -0.5],
[1.088_551_4, -1.025_773_4, -0.5],
[-1.3476, 0.816_000_04, -0.5],
[-0.874_034_4, -0.746_311_66, -0.5],
[-0.414_019_6, 0.457_632_04, -0.5],
[1.3476, -0.815_999_9, -0.5],
[0.874_034_64, 0.746_311_8, -0.5],
[0.414_019_44, -0.457_632_24, -0.5],
],
dtype=np.float32,
)
assert_allclose(snap.particles.position, manual)
def setup_thermo(request):
"""Test the initialisation of all crystals."""
with TemporaryDirectory() as tmp_dir:
output_dir = Path(tmp_dir) / "output"
output_dir.mkdir(exist_ok=True)
sim_params = SimulationParams(
temperature=0.4,
pressure=1.0,
num_steps=100,
crystal=request.param(),
output=output_dir,
cell_dimensions=(10, 12, 10),
outfile=output_dir / "test.gsd",
hoomd_args="--mode=cpu --notice-level=0",
)
context = hoomd.context.initialize(args=sim_params.hoomd_args)
sys = initialise_snapshot(
snapshot=init_from_crystal(sim_params),
context=context,
sim_params=sim_params,
thermalisation=True,
)
with context:
group = get_group(sys, sim_params)
integrator = set_integrator(sim_params, group)
thermo_log = hoomd.analyze.log(
None,
quantities=[
"translational_kinetic_energy",
"rotational_kinetic_energy",
"temperature",
],
period=1,
)
hoomd.run(1)
snap = sys.take_snapshot()
yield SimStatus(
sim_params=sim_params,
snapshot=snap,
context=context,
logger=thermo_log,
integrator=integrator,
system=sys,
)
def test_equilibrate(crystal_params, equil_type):
"""Ensure the equilibration is close to initialisation."""
# Initialisation of snapshot
snap_min = init_from_crystal(crystal_params)
# Equilibration
snapshot = equilibrate(snap_min, crystal_params, equil_type)
# Simulation box within 10% of initialisation
for attribute in ["Lx", "Ly", "Lz", "xy", "xz", "yz"]:
assert np.isclose(
getattr(snap_min.box, attribute),
getattr(snapshot.box, attribute),
rtol=0.20,
)
if equil_type in ["liquid", "interface"]:
assert snapshot.box.xy == 0
assert snapshot.box.xz == 0
assert snapshot.box.yz == 0
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)