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_hrex_save_and_load():
nc_filename = tempfile.mkdtemp() + "/out.nc"
temperature = 1 * unit.kelvin
powers = [2., 2., 4.]
n_replicas = len(powers)
oscillators = [
testsystems.PowerOscillator(b=powers[i]) for i in range(n_replicas)
]
systems = [ho.system for ho in oscillators]
positions = [ho.positions for ho in oscillators]
state = ThermodynamicState(system=systems[0], temperature=temperature)
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 200}
replica_exchange = hamiltonian_exchange.HamiltonianExchange.create(
state,
systems,
positions,
nc_filename,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
replica_exchange.extend(100)
replica_exchange = resume(nc_filename)
eq(replica_exchange.iteration, 200)
replica_exchange.run()
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
mpicomm = dummympi.DummyMPIComm()
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)
eq(replica_exchange.iteration, 200)
replica_exchange.run()
def test_check_positions():
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": 10}
replica_exchange = ReplicaExchange.create(states,
coordinates,
nc_filename,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
db = replica_exchange.database
db.check_energies()
def test_harmonic_oscillators_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
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 200}
replica_exchange = ReplicaExchange.create(states,
coordinates,
nc_filename,
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_parallel_tempering_explicit_temperature_input():
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
mpicomm = dummympi.DummyMPIComm()
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_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_power_oscillators():
nc_filename = tempfile.mkdtemp() + "/out.nc"
temperature = 1 * unit.kelvin
powers = [2., 2., 4.]
n_replicas = len(powers)
oscillators = [testsystems.PowerOscillator(b=powers[i]) for i in range(n_replicas)]
systems = [ho.system for ho in oscillators]
positions = [ho.positions for ho in oscillators]
state = ThermodynamicState(system=systems[0], temperature=temperature)
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations":2000}
replica_exchange = hamiltonian_exchange.HamiltonianExchange.create(state, systems, positions, 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)
beta = (state.temperature * kB) ** -1.
u0 = np.array([[testsystems.PowerOscillator.reduced_potential(beta, ho2.K, ho2.b, ho.K, ho.b) for ho in oscillators] for ho2 in oscillators])
l = np.log(u.mean(0))
l0 = np.log(u0)
eq(l0, l, decimal=1)
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)
def test_get_traj():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 300.0 * unit.kelvin
T_i = [T_min, T_min * 1.01, T_min * 1.1]
n_replicas = len(T_i)
ho = testsystems.AlanineDipeptideExplicit()
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": 3}
replica_exchange = ReplicaExchange.create(states,
coordinates,
nc_filename,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
db = replica_exchange.database
prmtop_filename = testsystems.get_data_filename(
"data/alanine-dipeptide-explicit/alanine-dipeptide.prmtop")
crd_filename = testsystems.get_data_filename(
"data/alanine-dipeptide-explicit/alanine-dipeptide.crd")
trj0 = md.load_restrt(crd_filename, top=prmtop_filename)
db.set_traj(trj0)
trj1 = db.get_traj(state_index=0)
trj2 = db.get_traj(replica_index=0)
