def setUp1(self, nproc=1, multiproc=True):
self.ndim = 3
self.harmonic = Harmonic(self.ndim)
self.nreplicas = 10
self.stepsize = 0.1
self.nproc = nproc
self.mc_runner = MonteCarloWalker(self.harmonic, mciter=40)
if multiproc == False:
hostname=socket.gethostname()
host = Pyro4.socketutil.getIpAddress(hostname, workaround127=True)
self.dispatcher_URI = "PYRO:"+"test@"+host+":9090"
else:
self.dispatcher_URI = None
replicas = []
for i in xrange(self.nreplicas):
x = self.harmonic.get_random_configuration()
replicas.append(Replica(x, self.harmonic.get_energy(x)))
self.ns = NestedSampling(replicas, self.mc_runner,
stepsize=0.1, nproc=nproc, verbose=False, dispatcher_URI=self.dispatcher_URI)
self.Emax0 = self.ns.replicas[-1].energy
self.niter = 100
for i in xrange(self.niter):
self.ns.one_iteration()
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
class TestNS_LJ(unittest.TestCase):
def setUp(self):
self.setUp1()
def compute_cv(self, Tmin=.01, Tmax=3., nT=100):
T = np.arange(Tmin, Tmax, (Tmax - Tmin) / nT)
Cv = compute_cv_c(np.array(self.ns.max_energies),
float(self.nproc), float(self.ndof), T.min(), T.max(), T.size, float(self.ndof), live=False)
return T, Cv
def set_up_system(self):
self.natoms = 13
self.gmin = -44.3269
self.system = LJClusterSENS(self.natoms, 2.5)
self.ndof = 3 * self.natoms - 6
def setUp1(self, nproc=1):
self.set_up_system()
self.nreplicas = 10
self.stepsize = 0.01
self.nproc = nproc
self.mc_runner = self.system.get_mc_walker(mciter=100)
self.ns = NestedSampling(self.system, self.nreplicas, self.mc_runner,
stepsize=0.1, nproc=nproc, verbose=False)
self.Emax0 = self.ns.replicas[-1].energy
self.niter = 100
for i in xrange(self.niter):
self.ns.one_iteration()
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def test1(self):
self.assert_(len(self.ns.replicas) == self.nreplicas)
self.assert_(self.Emax < self.Emax0)
self.assert_(self.Emin < self.Emax)
self.assert_(self.Emin < 0)
self.assert_(self.Emin >= self.gmin)
self.assert_(self.ns.stepsize != self.stepsize)
self.assertEqual(len(self.ns.max_energies), self.niter * self.nproc)
self.assertEqual(self.ns.failed_mc_walks, 0)
def run_ns(self, max_iter=100, Etol=1e-4):
# max_iter = 10000
# self.Etol = .01
self.Etol = Etol
for i in xrange(int(max_iter)):
self.ns.one_iteration()
deltaE = self.ns.replicas[-1].energy - self.ns.replicas[0].energy
if deltaE < self.Etol:
break
self.niter = i + 1
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def finish(self):
NestedSampling.finish(self)
if self.nproc > 1:
# terminate the swap workers
for worker in self._swap_workers:
self._swap_put_queue.put("kill")
for worker in self._swap_workers:
worker.join()
worker.terminate()
worker.join()
def do_nested_sampling(nreplicas=10, niter=200, mciter=1000, stepsize=.8, estop=-.9,
x0=[1,1], r0=2,
xlim=None, ylim=None, circle=False
):
path = []
def mc_record_position_event(coords=None, **kwargs):
if len(path) == 0 or not np.all(path[-1] == coords):
path.append(coords)
p = Pot()
print p.get_energy(np.array([1,2.]))
mc_walker = MonteCarloWalker(p, mciter=mciter, events=[mc_record_position_event])
# initialize the replicas with random positions
replicas = []
for i in xrange(nreplicas):
# choose points uniformly in a circle
if circle:
coords = vector_random_uniform_hypersphere(2) * r0 + x0
else:
coords = np.zeros(2)
coords[0] = np.random.uniform(xlim[0], xlim[1])
coords[1] = np.random.uniform(ylim[0], ylim[1])
# coords = np.random.uniform(-1,3,size=2)
r = Replica(coords, p.get_energy(coords))
replicas.append(r)
ns = NestedSampling(replicas, mc_walker, stepsize=stepsize)
results = [Result()]
results[0].replicas = [r.copy() for r in replicas]
for i in xrange(niter):
ns.one_iteration()
new_res = Result()
new_res.replicas = [r.copy() for r in replicas]
new_res.starting_replica = ns.starting_replicas[0].copy()
new_res.new_replica = ns.new_replicas[0].copy()
path.insert(0, new_res.starting_replica.x)
new_res.mc_path = path
results.append(new_res)
path = []
if ns.replicas[-1].energy < estop:
break
# plt.plot(ns.max_energies)
# plt.show()
return ns, results
class TestNS(unittest.TestCase):
"""to test distributed computing must start a dispatcher with --server-name test and --port 9090
"""
def setUp(self):
self.setUp1()
def setUp1(self, nproc=1, multiproc=True):
self.ndim = 3
self.harmonic = Harmonic(self.ndim)
self.nreplicas = 10
self.stepsize = 0.1
self.nproc = nproc
self.mc_runner = MonteCarloWalker(self.harmonic, mciter=40)
if multiproc == False:
hostname = socket.gethostname()
host = Pyro4.socketutil.getIpAddress(hostname, workaround127=True)
self.dispatcher_URI = "PYRO:" + "test@" + host + ":9090"
else:
self.dispatcher_URI = None
replicas = []
for i in range(self.nreplicas):
x = self.harmonic.get_random_configuration()
replicas.append(Replica(x, self.harmonic.get_energy(x)))
self.ns = NestedSampling(replicas,
self.mc_runner,
stepsize=0.1,
nproc=nproc,
verbose=False,
dispatcher_URI=self.dispatcher_URI)
self.Emax0 = self.ns.replicas[-1].energy
self.niter = 100
for i in range(self.niter):
self.ns.one_iteration()
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def test1(self):
print("running TestNS")
self.assert_(len(self.ns.replicas) == self.nreplicas)
self.assert_(self.Emax < self.Emax0)
self.assert_(self.Emin < self.Emax)
self.assert_(self.Emin >= 0)
self.assert_(self.ns.stepsize != self.stepsize)
self.assertEqual(len(self.ns.max_energies), self.niter * self.nproc)
class TestNS(unittest.TestCase):
"""to test distributed computing must start a dispatcher with --server-name test and --port 9090
"""
def setUp(self):
self.setUp1()
def setUp1(self, nproc=1, multiproc=True):
self.ndim = 3
self.harmonic = Harmonic(self.ndim)
self.nreplicas = 10
self.stepsize = 0.1
self.nproc = nproc
self.mc_runner = MonteCarloWalker(self.harmonic, mciter=40)
if multiproc == False:
hostname=socket.gethostname()
host = Pyro4.socketutil.getIpAddress(hostname, workaround127=True)
self.dispatcher_URI = "PYRO:"+"test@"+host+":9090"
else:
self.dispatcher_URI = None
replicas = []
for i in xrange(self.nreplicas):
x = self.harmonic.get_random_configuration()
replicas.append(Replica(x, self.harmonic.get_energy(x)))
self.ns = NestedSampling(replicas, self.mc_runner,
stepsize=0.1, nproc=nproc, verbose=False, dispatcher_URI=self.dispatcher_URI)
self.Emax0 = self.ns.replicas[-1].energy
self.niter = 100
for i in xrange(self.niter):
self.ns.one_iteration()
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def test1(self):
print "running TestNS"
self.assert_(len(self.ns.replicas) == self.nreplicas)
self.assert_(self.Emax < self.Emax0)
self.assert_(self.Emin < self.Emax)
self.assert_(self.Emin >= 0)
self.assert_(self.ns.stepsize != self.stepsize)
self.assertEqual(len(self.ns.max_energies), self.niter * self.nproc)
def setUp1(self, nproc=1):
self.set_up_system()
self.nreplicas = 10
self.stepsize = 0.01
self.nproc = nproc
self.mc_runner = self.system.get_mc_walker(mciter=100)
self.ns = NestedSampling(self.system,
self.nreplicas,
self.mc_runner,
stepsize=0.1,
nproc=nproc,
verbose=False)
self.Emax0 = self.ns.replicas[-1].energy
self.niter = 100
for i in xrange(self.niter):
self.ns.one_iteration()
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def setUp1(self, nproc=1):
self.set_up_system()
self.nreplicas = 10
self.stepsize = 0.01
self.nproc = nproc
self.mc_runner = self.system.get_mc_walker(mciter=100)
self.ns = NestedSampling(self.system, self.nreplicas, self.mc_runner,
stepsize=0.1, nproc=nproc, verbose=False)
self.Emax0 = self.ns.replicas[-1].energy
self.niter = 100
for i in xrange(self.niter):
self.ns.one_iteration()
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def setUp1(self, nproc=4):
self.set_up_system()
self.nreplicas = 50
self.stepsize = 0.01
self.nproc = nproc
self.mc_runner = self.system.get_mc_walker(mciter=10000)
self.ns = NestedSampling(self.system,
self.nreplicas,
self.mc_runner,
stepsize=self.stepsize,
nproc=nproc,
verbose=True,
iprint=100)
self.Emax0 = self.ns.replicas[-1].energy
self.run_ns(max_iter=10000, Etol=.01)
def main():
parser = argparse.ArgumentParser(
description=
"do nested sampling on a p[article in a n-dimensional Harmonic well")
# parser.add_argument("--db", type=str, nargs=1, help="database filename",
# default="otp.db")
parser.add_argument("-K",
"--nreplicas",
type=int,
help="number of replicas",
default=300)
parser.add_argument("-A",
"--ndof",
type=int,
help="number of degrees of freedom",
default=4)
parser.add_argument("-P",
"--nproc",
type=int,
help="number of processors",
default=1)
parser.add_argument("--trivparal",
action='store_true',
help="set whether to do trivial parallelisation",
default=False)
parser.add_argument(
"-q",
action="store_true",
help="turn off verbose printing of information at every step")
args = parser.parse_args()
system = HarParticle(args.ndof, Emax_init=1000.)
mcrunner = HarRunner(system)
# ns = NestedSamplingSerial(system, args.nreplicas, mcrunner,
# verbose=not args.q)
ns = NestedSampling(system,
args.nreplicas,
mcrunner,
nproc=args.nproc,
triv_paral=args.trivparal,
verbose=not args.q)
print "harmonic particle ndof", args.ndof
run_nested_sampling(ns, label="hparticle", etol=.00000001)
def setUp1(self, nproc=1):
self.ndim = 3
self.harmonic = Harmonic(self.ndim)
self.nreplicas = 10
self.stepsize = 0.1
self.nproc = nproc
self.mc_runner = MonteCarloWalker(self.harmonic, mciter=40)
replicas = []
for i in range(self.nreplicas):
x = self.harmonic.get_random_configuration()
replicas.append(Replica(x, self.harmonic.get_energy(x)))
self.ns = NestedSampling(replicas, self.mc_runner,
stepsize=0.1, nproc=nproc, verbose=False)
self.etol = 0.01
run_nested_sampling(self.ns, label="test", etol=self.etol)
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def main():
parser = argparse.ArgumentParser(description="do nested sampling on a p[article in a n-dimensional Harmonic well")
parser.add_argument("-K", "--nreplicas", type=float, help="number of replicas", default=1e1)
parser.add_argument("-A", "--ndof", type=int, help="number of degrees of freedom", default=3)
parser.add_argument("-P", "--nproc", type=int, help="number of processors", default=1)
parser.add_argument("-N", "--nsteps", type=int, help="number of MC steps per NS iteration", default=int(1e3))
parser.add_argument("--stepsize", type=float, help="stepsize, adapted between NS iterations", default=20)
parser.add_argument("--etol", type=float, help="energy tolerance: the calculation terminates when the energy difference \
between Emax and Emin is less than etol", default=0.1)
parser.add_argument("-q", action="store_true", help="turn off verbose printing of information at every step")
args = parser.parse_args()
ndof = args.ndof
nproc = args.nproc
nsteps = int(args.nsteps)-8
nreplicas = int(args.nreplicas)
stepsize = args.stepsize
etol = args.etol
#construct potential (cost function)
potential = Harmonic(ndof)
#construct Monte Carlo walker
mc_runner = MonteCarloWalker(potential, mciter=nsteps)
#initialise replicas (initial uniformly samples set of configurations)
replicas = []
for _ in range(nreplicas):
x = potential.get_random_configuration()
print(x)
print(potential.get_energy(x))
replicas.append(Replica(x, potential.get_energy(x)))
#construct Nested Sampling object
ns = NestedSampling(replicas, mc_runner, stepsize=stepsize, nproc=nproc, max_stepsize=10, verbose=not args.q)
#run Nested Sampling (NS), output:
## label.energies (one for each iteration)
## label.replicas_final (live replica energies when NS terminates)
run_nested_sampling(ns, label="run_hparticle", etol=etol)
def main():
parser = argparse.ArgumentParser(
description=
"do nested sampling on a p[article in a n-dimensional Harmonic well")
parser.add_argument("-K",
"--nreplicas",
type=int,
help="number of replicas",
default=300)
parser.add_argument("-A",
"--ndof",
type=int,
help="number of degrees of freedom",
default=4)
parser.add_argument("-P",
"--nproc",
type=int,
help="number of processors",
default=1)
parser.add_argument("-N",
"--nsteps",
type=int,
help="number of MC steps per NS iteration",
default=100)
parser.add_argument("--stepsize",
type=float,
help="stepsize, adapted between NS iterations",
default=0.1)
parser.add_argument(
"--etol",
type=float,
help=
"energy tolerance: the calculation terminates when the energy difference \
between Emax and Emin is less than etol",
default=0.01)
parser.add_argument(
"-q",
action="store_true",
help="turn off verbose printing of information at every step")
parser.add_argument(
"--dispatcherURI",
action="store_true",
help="use URI of the dispatcher server in default location",
default=False)
parser.add_argument(
"--dispatcherURI-file",
type=str,
help="use URI of the dispatcher server if different from default",
default=None)
#set basic parameters
args = parser.parse_args()
ndof = args.ndof
nproc = args.nproc
nsteps = args.nsteps
nreplicas = args.nreplicas
stepsize = args.stepsize
etol = args.etol
#try to read dispatecher URI from default file location
if args.dispatcherURI is True:
with open("dispatcher_uri.dat", "r") as rfile:
dispatcherURI = rfile.read().replace('\n', '')
elif args.dispatcherURI_file != None:
with open(args.dispatcherURI_file, "r") as rfile:
dispatcherURI = rfile.read().replace('\n', '')
else:
dispatcherURI = None
#construct potential (cost function)
potential = Harmonic(ndof)
#construct Monte Carlo walker
mc_runner = MonteCarloWalker(potential, mciter=nsteps)
#initialise replicas (initial uniformly samples set of configurations)
replicas = []
for _ in xrange(nreplicas):
x = potential.get_random_configuration()
replicas.append(Replica(x, potential.get_energy(x)))
#construct Nested Sampling object and pass dispatcher address
ns = NestedSampling(replicas,
mc_runner,
stepsize=stepsize,
nproc=nproc,
dispatcher_URI=dispatcherURI,
max_stepsize=10,
verbose=not args.q)
#run Nested Sampling (NS), output:
## label.energies (one for each iteration)
## label.replicas_final (live replica energies when NS terminates)
run_nested_sampling(ns, label="run_hparticle", etol=etol)
class TestNS_LJ(unittest.TestCase):
def setUp(self):
self.setUp1()
def compute_cv(self, Tmin=.01, Tmax=3., nT=100):
T = np.arange(Tmin, Tmax, (Tmax - Tmin) / nT)
Cv = compute_cv_c(np.array(self.ns.max_energies),
float(self.nproc),
float(self.ndof),
T.min(),
T.max(),
T.size,
float(self.ndof),
live=False)
return T, Cv
def set_up_system(self):
self.natoms = 13
self.gmin = -44.3269
self.system = LJClusterSENS(self.natoms, 2.5)
self.ndof = 3 * self.natoms - 6
def setUp1(self, nproc=1):
self.set_up_system()
self.nreplicas = 10
self.stepsize = 0.01
self.nproc = nproc
self.mc_runner = self.system.get_mc_walker(mciter=100)
self.ns = NestedSampling(self.system,
self.nreplicas,
self.mc_runner,
stepsize=0.1,
nproc=nproc,
verbose=False)
self.Emax0 = self.ns.replicas[-1].energy
self.niter = 100
for i in xrange(self.niter):
self.ns.one_iteration()
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def test1(self):
self.assert_(len(self.ns.replicas) == self.nreplicas)
self.assert_(self.Emax < self.Emax0)
self.assert_(self.Emin < self.Emax)
self.assert_(self.Emin < 0)
self.assert_(self.Emin >= self.gmin)
self.assert_(self.ns.stepsize != self.stepsize)
self.assertEqual(len(self.ns.max_energies), self.niter * self.nproc)
self.assertEqual(self.ns.failed_mc_walks, 0)
def run_ns(self, max_iter=100, Etol=1e-4):
# max_iter = 10000
# self.Etol = .01
self.Etol = Etol
for i in xrange(int(max_iter)):
self.ns.one_iteration()
deltaE = self.ns.replicas[-1].energy - self.ns.replicas[0].energy
if deltaE < self.Etol:
break
self.niter = i + 1
self.Emax = self.ns.replicas[-1].energy
self.Emin = self.ns.replicas[0].energy
def run_nested_sampling_lj(system,
nreplicas=300,
mciter=1000,
target_ratio=0.7,
label="test",
minima=None,
use_compiled=True,
nproc=1,
triv_paral=True,
minprob=1,
maxiter=1e100,
**kwargs):
takestep = RandomDisplacement(stepsize=0.07)
accept_tests = system.get_config_tests()
if type(system) is LJClusterNew:
if use_compiled:
mc_runner = MonteCarloCompiled(system.radius)
# import pickle
# with open("testpickle", "w") as pout:
# pickle.dump(mc_runner, pout)
else:
mc_runner = MonteCarloChain(system.get_potential(),
takestep,
accept_tests=accept_tests)
print "using the compiled MC = ", use_compiled
elif type(system) is HarParticle:
mc_runner = HarRunner(system)
print "using HarRunner"
elif type(system) is IsingSystem:
mc_runner = IsingRunnerC(system)
print "using IsingRunner"
else:
raise TypeError('system type is not known')
print "using", nproc, "processors"
if minima is not None:
assert (len(minima) > 0)
print "using", len(minima), "minima"
ns = NestedSamplingBS(system,
nreplicas,
mc_runner,
minima,
mciter=mciter,
target_ratio=target_ratio,
stepsize=0.07,
nproc=nproc,
triv_paral=triv_paral,
minprob=minprob,
**kwargs)
else:
ns = NestedSampling(system,
nreplicas,
mc_runner,
mciter=mciter,
target_ratio=target_ratio,
stepsize=0.07,
nproc=nproc,
triv_paral=triv_paral,
**kwargs)
etol = 0.01
ns = run_nested_sampling(ns, label, etol, maxiter=maxiter)
return ns