def test_logging():
logging_check(
hoomd.hpmc.compute.FreeVolume, ('hpmc', 'compute'),
{'free_volume': {
'category': LoggerCategories.scalar,
'default': True
}})
def test_logging(simulation_factory, two_particle_snapshot_factory):
filt = hoomd.filter.All()
T = 1.0
thermoHMA = hoomd.md.compute.HarmonicAveragedThermodynamicQuantities(
filt, T)
snap = two_particle_snapshot_factory()
if snap.communicator.rank == 0:
snap.particles.velocity[:] = [[-2, 0, 0], [2, 0, 0]]
sim = simulation_factory(snap)
sim.always_compute_pressure = True
sim.operations.add(thermoHMA)
integrator = hoomd.md.Integrator(dt=0.0001)
integrator.methods.append(hoomd.md.methods.NVT(filt, tau=1, kT=T))
sim.operations.integrator = integrator
log = hoomd.logging.Logger()
log += thermoHMA
sim.run(5)
logging_check(
hoomd.md.compute.HarmonicAveragedThermodynamicQuantities,
('md', 'compute'), {
'potential_energy': {
'category': LoggerCategories.scalar,
'default': True
},
'pressure': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging():
base_loggables = {
'shortest_rebuild': {
'category': LoggerCategories.scalar,
'default': True
},
'num_builds': {
'category': LoggerCategories.scalar,
'default': False
}
}
logging_check(hoomd.md.nlist.NeighborList, ('md', 'nlist'), base_loggables)
logging_check(
hoomd.md.nlist.Cell, ('md', 'nlist'), {
**base_loggables,
'dimensions': {
'category': LoggerCategories.sequence,
'default': False
},
'allocated_particles_per_cell': {
'category': LoggerCategories.scalar,
'default': False
},
})
def test_logging():
logging_check(hoomd.md.nlist.NList, ('md', 'nlist'), {
'shortest_rebuild': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging():
logging_check(hoomd.hpmc.update.Clusters, ('hpmc', 'update'), {
'avg_cluster_size': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging():
logging_check(
hoomd.md.update.ReversePerturbationFlow, ('md', 'update'), {
'summed_exchanged_momentum': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging():
logging_check(
hoomd.hpmc.compute.SDF, ('hpmc', 'compute'), {
'betaP': {
'category': LoggerCategories.scalar,
'default': True
},
'sdf': {
'category': LoggerCategories.sequence,
'default': True
}
})
def test_logging():
logging_check(
hoomd.md.minimize.FIRE, ('md', 'minimize', 'fire'), {
'converged': {
'category': LoggerCategories.scalar,
'default': False
},
'energy': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging():
logging_check(
hoomd.md.compute.ThermodynamicQuantities, ('md', 'compute'), {
'kinetic_temperature': {
'category': LoggerCategories.scalar,
'default': True
},
'pressure': {
'category': LoggerCategories.scalar,
'default': True
},
'pressure_tensor': {
'category': LoggerCategories.sequence,
'default': True
},
'kinetic_energy': {
'category': LoggerCategories.scalar,
'default': True
},
'translational_kinetic_energy': {
'category': LoggerCategories.scalar,
'default': True
},
'rotational_kinetic_energy': {
'category': LoggerCategories.scalar,
'default': True
},
'potential_energy': {
'category': LoggerCategories.scalar,
'default': True
},
'degrees_of_freedom': {
'category': LoggerCategories.scalar,
'default': True
},
'translational_degrees_of_freedom': {
'category': LoggerCategories.scalar,
'default': True
},
'rotational_degrees_of_freedom': {
'category': LoggerCategories.scalar,
'default': True
},
'num_particles': {
'category': LoggerCategories.scalar,
'default': True
},
'volume': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging():
logging_check(
hoomd.md.compute.HarmonicAveragedThermodynamicQuantities,
('md', 'compute'), {
'potential_energy': {
'category': LoggerCategories.scalar,
'default': True
},
'pressure': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging():
logging_check(
hoomd.hpmc.update.BoxMC, ('hpmc', 'update'), {
'aspect_moves': {
'category': LoggerCategories.sequence,
'default': True
},
'shear_moves': {
'category': LoggerCategories.sequence,
'default': True
},
'volume_moves': {
'category': LoggerCategories.sequence,
'default': True
}
})
def test_logging(self):
expected_namespace = ("pytest", "test_custom_writer")
conftest.logging_check(
WriteTimestep, ("pytest", "test_custom_writer"), {
"fourty_two": {
"category": hoomd.logging.LoggerCategories.scalar,
"default": True
}
})
writer = hoomd.write.CustomWriter(2, WriteTimestep())
# Check namespace
log_quantity = writer._export_dict["fourty_two"]
assert log_quantity.namespace == expected_namespace + (
WriteTimestep.__name__, )
assert log_quantity.default
assert log_quantity.category == hoomd.logging.LoggerCategories.scalar
def test_logging():
logging_check(
hoomd.hpmc.integrate.HPMCIntegrator, ('hpmc', 'integrate'), {
'map_overlaps': {
'category': LoggerCategories.sequence,
'default': True
},
'mps': {
'category': LoggerCategories.scalar,
'default': True
},
'overlaps': {
'category': LoggerCategories.scalar,
'default': True
},
'rotate_moves': {
'category': LoggerCategories.sequence,
'default': True
},
'translate_moves': {
'category': LoggerCategories.sequence,
'default': True
}
})
integrators = (hoomd.hpmc.integrate.Sphere,
hoomd.hpmc.integrate.ConvexPolygon,
hoomd.hpmc.integrate.ConvexSpheropolygon,
hoomd.hpmc.integrate.Polyhedron,
hoomd.hpmc.integrate.ConvexPolyhedron,
hoomd.hpmc.integrate.ConvexSpheropolyhedron,
hoomd.hpmc.integrate.Ellipsoid,
hoomd.hpmc.integrate.SphereUnion)
type_shapes_check = {
'type_shapes': {
'category': LoggerCategories.object,
'default': True
}
}
for integrator in integrators:
logging_check(integrator, ('hpmc', 'integrate'), type_shapes_check)
def test_logging():
logging_check(hoomd.md.methods.NPH, ('md', 'methods'), {
'barostat_energy': {
'category': LoggerCategories.scalar,
'default': True
}
})
logging_check(
hoomd.md.methods.NPT, ('md', 'methods'), {
'barostat_energy': {
'category': LoggerCategories.scalar,
'default': True
},
'thermostat_energy': {
'category': LoggerCategories.scalar,
'default': True
}
})
logging_check(
hoomd.md.methods.NVT, ('md', 'methods'), {
'thermostat_energy': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging():
logging_check(
hoomd.Simulation, (), {
'final_timestep': {
'category': LoggerCategories.scalar,
'default': True
},
'seed': {
'category': LoggerCategories.scalar,
'default': True
},
'timestep': {
'category': LoggerCategories.scalar,
'default': True
},
'tps': {
'category': LoggerCategories.scalar,
'default': True
},
'walltime': {
'category': LoggerCategories.scalar,
'default': True
}
})
def test_logging(cls, expected_namespace, expected_loggables):
logging_check(cls, expected_namespace, expected_loggables)
def test_logging(cls, log_check_params):
logging_check(cls, ('md', 'pair', 'aniso'), log_check_params)
