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_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_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_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_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_all_testsystems():
T_min = 1.0 * u.kelvin
T_max = 10.0 * u.kelvin
n_temps = 3
testsystem_classes = testsystems.TestSystem.__subclasses__()
for testsystem_class in testsystem_classes:
class_name = testsystem_class.__name__
if class_name in fast_testsystems:
logging.info("Testing replica exchange with testsystem %s" %
class_name)
else:
logging.info("Skipping replica exchange with testsystem %s." %
class_name)
continue
testsystem = testsystem_class()
system = testsystem.system
positions = [testsystem.positions] * n_temps
nc_filename = tempfile.mkdtemp() + "/out.nc"
parameters = {"number_of_iterations": 3}
replica_exchange = ParallelTempering.create(system,
positions,
nc_filename,
T_min=T_min,
T_max=T_max,
n_temps=n_temps,
parameters=parameters)
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_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_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_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_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 notest_parallel_tempering_all_testsystems():
T_min = 1.0 * u.kelvin
T_max = 10.0 * u.kelvin
n_temps = 3
testsystem_classes = testsystems.TestSystem.__subclasses__()
for testsystem_class in testsystem_classes:
class_name = testsystem_class.__name__
if class_name in fast_testsystems:
logging.info("Testing replica exchange with testsystem %s" % class_name)
else:
logging.info("Skipping replica exchange with testsystem %s." % class_name)
continue
testsystem = testsystem_class()
system = testsystem.system
positions = [testsystem.positions] * n_temps
nc_filename = tempfile.mkdtemp() + "/out.nc"
parameters = {"number_of_iterations":3}
replica_exchange = ParallelTempering.create(system, positions, nc_filename, T_min=T_min, T_max=T_max, n_temps=n_temps, parameters=parameters)
replica_exchange.run()
import simtk.unit as u
from simtk.openmm import app
import simtk.openmm as mm
from repex.thermodynamics import ThermodynamicState
from repex.parallel_tempering import ParallelTempering
import repex.netcdf_io
from mpi4py import MPI # MPI wrapper
name = "1vii"
equil_filename = "./equil/%s.pdb" % name
nc_filename = "./%s.nc" % name
n_replicas = 50 # number of temperature replicas
T_min = 300.0 * u.kelvin # minimum temperature
T_max = 450.0 * u.kelvin # maximum temperature
parameters = dict(pressure=1.0 * u.atmospheres, number_of_iterations=1000)
T_i = [ T_min + (T_max - T_min) * (np.exp(float(i) / float(n_replicas-1)) - 1.0) / (np.e - 1.0) for i in range(n_replicas)]
forcefield = app.ForceField("amber10.xml", "tip3p.xml")
pdb = app.PDBFile(equil_filename)
system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.CutoffPeriodic, nonbondedCutoff=1.0 * u.nanometers, constraints=app.HBonds)
coordinates = [pdb.positions] * n_replicas
rex = ParallelTempering.create(system, coordinates, nc_filename, T_min=T_min, T_max=T_max, n_temps=n_replicas, mpicomm=MPI.COMM_WORLD, parameters=parameters)
rex.run()
