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)