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_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():
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_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_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
trj0 = md.load("repex/data/alanine-dipeptide-explicit/alanine-dipeptide.pdb")
db.set_traj(trj0)
trj1 = db.get_traj(state_index=0)
trj2 = db.get_traj(replica_index=0)
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_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)
