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)