def test_parallel_tempering_save_and_load(mpicomm):
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_max = 10.0 * unit.kelvin
n_temps = 3
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
coordinates = [positions] * n_temps
parameters = {"number_of_iterations": 200}
replica_exchange = ParallelTempering.create(system,
coordinates,
nc_filename,
T_min=T_min,
T_max=T_max,
n_temps=n_temps,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
replica_exchange.extend(100)
replica_exchange = resume(nc_filename, mpicomm=mpicomm)
eq(replica_exchange.iteration, 200)
replica_exchange.run()
def test_double_set_thermodynamic_states():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_max = 10.0 * unit.kelvin
n_temps = 3
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
coordinates = [positions] * n_temps
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 3}
replica_exchange = ParallelTempering.create(system,
coordinates,
nc_filename,
T_min=T_min,
T_max=T_max,
n_temps=n_temps,
mpicomm=mpicomm,
parameters=parameters)
eq(replica_exchange.n_replicas, n_temps)
replica_exchange.run()
states = replica_exchange.thermodynamic_states
replica_exchange.database.thermodynamic_states = states
def test_parallel_tempering_explicit_temperature_input(mpicomm):
nc_filename = tempfile.mkdtemp() + "/out.nc"
T0 = 1.0 * unit.kelvin
temperatures = [T0, T0 * 2, T0 * 4]
n_temps = len(temperatures)
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
coordinates = [positions] * n_temps
parameters = {"number_of_iterations": 100}
replica_exchange = ParallelTempering.create(system,
coordinates,
nc_filename,
temperatures=temperatures,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
eq(replica_exchange.n_replicas, n_temps)
def test_repex_save_and_load():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_i = [T_min, T_min * 10., T_min * 100.]
n_replicas = len(T_i)
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
states = [
ThermodynamicState(system=system, temperature=T_i[i])
for i in range(n_replicas)
]
coordinates = [positions] * n_replicas
parameters = {"number_of_iterations": 5}
rex = replica_exchange.ReplicaExchange.create(states,
coordinates,
nc_filename,
parameters=parameters)
rex.run()
rex.extend(5)
rex = resume(nc_filename)
rex.run()
eq(rex.__class__.__name__, "ReplicaExchange")
def test_parallel_tempering_save_and_load():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_max = 10.0 * unit.kelvin
n_temps = 3
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
coordinates = [positions] * n_temps
parameters = {"number_of_iterations": 5}
rex = parallel_tempering.ParallelTempering.create(system,
coordinates,
nc_filename,
T_min=T_min,
T_max=T_max,
n_temps=n_temps,
parameters=parameters)
rex.run()
rex.extend(5)
rex = resume(nc_filename)
rex.run()
eq(rex.__class__.__name__, "ParallelTempering")
def test_harmonic_oscillators_fewer_coordinates_than_states():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_i = [T_min, T_min * 10., T_min * 100.]
n_replicas = len(T_i)
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
states = [
ThermodynamicState(system=system, temperature=T_i[i])
for i in range(n_replicas)
]
coordinates = [positions]
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 10}
replica_exchange = ReplicaExchange.create(states,
coordinates,
nc_filename,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
def test_parallel_tempering_pressure():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_max = 10.0 * unit.kelvin
n_temps = 3
pressure = 1.0 * unit.atmospheres
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
coordinates = [positions] * n_temps
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 4}
replica_exchange = ParallelTempering.create(system,
coordinates,
nc_filename,
T_min=T_min,
T_max=T_max,
n_temps=n_temps,
pressure=pressure,
mpicomm=mpicomm,
parameters=parameters)
eq(replica_exchange.n_replicas, n_temps)
replica_exchange.run()
def test_harmonic_oscillators_save_and_load(mpicomm):
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_i = [T_min, T_min * 10., T_min * 100.]
n_replicas = len(T_i)
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
states = [
ThermodynamicState(system=system, temperature=T_i[i])
for i in range(n_replicas)
]
coordinates = [positions] * n_replicas
parameters = {"number_of_iterations": 50}
replica_exchange = ReplicaExchange.create(states,
coordinates,
nc_filename,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
replica_exchange.extend(50)
replica_exchange = resume(nc_filename, mpicomm=mpicomm)
replica_exchange.run()
def test_output_diagnostics():
tempdir = tempfile.mkdtemp()
nc_filename = tempdir + "/out.nc"
T_min = 1.0 * unit.kelvin
T_i = [T_min, T_min * 10., T_min * 100.]
n_replicas = len(T_i)
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
states = [
ThermodynamicState(system=system, temperature=T_i[i])
for i in range(n_replicas)
]
coordinates = [positions] * n_replicas
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 10}
replica_exchange = ReplicaExchange.create(states,
coordinates,
nc_filename,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
db = replica_exchange.database
db.check_energies()
db.output_diagnostics(tempdir + "/diagnostics/")
def test_repex_multiple_save_and_load():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_i = [T_min, T_min * 2.0, T_min * 2.0]
n_replicas = len(T_i)
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
states = [
ThermodynamicState(system=system, temperature=T_i[i])
for i in range(n_replicas)
]
coordinates = [positions] * n_replicas
parameters = {"number_of_iterations": steps}
rex = replica_exchange.ReplicaExchange.create(states,
coordinates,
nc_filename,
parameters=parameters)
rex.run()
for repeat in range(repeats):
replica_states0 = rex.replica_states
Nij_proposed0 = rex.Nij_proposed
Nij_accepted0 = rex.Nij_accepted
sampler_states0 = rex.sampler_states
rex.extend(steps)
rex = resume(nc_filename)
replica_states1 = rex.replica_states
Nij_proposed1 = rex.Nij_proposed
Nij_accepted1 = rex.Nij_accepted
sampler_states1 = rex.sampler_states
eq(replica_states0, replica_states1)
eq(Nij_proposed0, Nij_proposed1)
eq(Nij_accepted0, Nij_accepted1)
rex.run()
def test_parallel_tempering_multiple_save_and_load():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_max = 2.0 * unit.kelvin
n_temps = 3
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
coordinates = [positions] * n_temps
parameters = {"number_of_iterations": steps}
rex = parallel_tempering.ParallelTempering.create(system,
coordinates,
nc_filename,
T_min=T_min,
T_max=T_max,
n_temps=n_temps,
parameters=parameters)
rex.run()
for repeat in range(repeats):
replica_states0 = rex.replica_states
Nij_proposed0 = rex.Nij_proposed
Nij_accepted0 = rex.Nij_accepted
sampler_states0 = rex.sampler_states
rex.extend(steps)
rex = resume(nc_filename)
replica_states1 = rex.replica_states
Nij_proposed1 = rex.Nij_proposed
Nij_accepted1 = rex.Nij_accepted
sampler_states1 = rex.sampler_states
eq(replica_states0, replica_states1)
eq(Nij_proposed0, Nij_proposed1)
eq(Nij_accepted0, Nij_accepted1)
rex.run()
def test_parallel_tempering():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_max = 10.0 * unit.kelvin
n_temps = 3
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
coordinates = [positions] * n_temps
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 1000}
replica_exchange = ParallelTempering.create(system,
coordinates,
nc_filename,
T_min=T_min,
T_max=T_max,
n_temps=n_temps,
mpicomm=mpicomm,
parameters=parameters)
eq(replica_exchange.n_replicas, n_temps)
replica_exchange.run()
u_permuted = replica_exchange.database.ncfile.variables["energies"][:]
s = replica_exchange.database.ncfile.variables["states"][:]
u = permute_energies(u_permuted, s)
states = replica_exchange.thermodynamic_states
u0 = np.array([[ho.reduced_potential_expectation(s0, s1) for s1 in states]
for s0 in states])
l0 = np.log(
u0
) # Compare on log scale because uncertainties are proportional to values
l1 = np.log(u.mean(0))
eq(l0, l1, decimal=1)
def test_harmonic_oscillators():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 1.0 * unit.kelvin
T_i = [T_min, T_min * 10., T_min * 100.]
n_replicas = len(T_i)
ho = testsystems.HarmonicOscillator()
system = ho.system
positions = ho.positions
states = [
ThermodynamicState(system=system, temperature=T_i[i])
for i in range(n_replicas)
]
coordinates = [positions] * n_replicas
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 1000}
replica_exchange = ReplicaExchange.create(states,
coordinates,
nc_filename,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
u_permuted = replica_exchange.database.ncfile.variables["energies"][:]
s = replica_exchange.database.ncfile.variables["states"][:]
u = permute_energies(u_permuted, s)
u0 = np.array([[ho.reduced_potential_expectation(s0, s1) for s1 in states]
for s0 in states])
l0 = np.log(
u0
) # Compare on log scale because uncertainties are proportional to values
l1 = np.log(u.mean(0))
eq(l0, l1, decimal=1)
tolerance = 1.0e-8 # constraint tolerance nsteps = 1000 # number of timesteps per iteration nequil = 50 # number of equilibration iterations niterations = 100 # number of production iterations # Select system: #testsystem = testsystems.MolecularIdealGas() #testsystem = testsystems.AlanineDipeptideVacuum(constraints=None) #testsystem = testsystems.AlanineDipeptideVacuum(constraints=app.HBonds) #testsystem = testsystems.AlanineDipeptideImplicit(constraints=app.HBonds) #testsystem = testsystems.AlanineDipeptideExplicit(constraints=app.HBonds, rigid_water=True) #testsystem = testsystems.Diatom(constraint=True, use_central_potential=True) #testsystem = testsystems.ConstraintCoupledHarmonicOscillator() #testsystem = testsystems.LysozymeImplicit(flexibleConstraints=False, shake=True) testsystem = testsystems.HarmonicOscillator() #testsystem = testsystems.HarmonicOscillatorArray(N=16) #testsystem = testsystems.WaterBox(constrain=True, flexible=False) # Retrieve system and positions. [system, positions] = [testsystem.system, testsystem.positions] #velocities = generateMaxwellBoltzmannVelocities(system, temperature) ndof = 3 * system.getNumParticles() - system.getNumConstraints() # Select integrator: #integrator = openmm.LangevinIntegrator(temperature, collision_rate, timestep) #integrator = integrators.AndersenVelocityVerletIntegrator(temperature=temperature, timestep=timestep) #integrator = integrators.MetropolisMonteCarloIntegrator(timestep=timestep, temperature=temperature, sigma=0.01*units.angstroms) #integrator = integrators.HMCIntegrator(timestep=timestep, temperature=temperature) #integrator = integrators.VVVRIntegrator(timestep=timestep, temperature=temperature, collision_rate=collision_rate)
