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("-q", action="store_true", help="turn off verbose printing of information at every step")
args = parser.parse_args()
system = Harmonic(args.ndof)
mcrunner = HarmonicSampler(system, args.ndof)
ns = NestedSampling(system, args.nreplicas, mcrunner, nproc=args.nproc, verbose=not args.q)
print "harmonic particle ndof", args.ndof
run_nested_sampling(ns, label="hparticle", etol=1e-5)
def main():
parser = argparse.ArgumentParser(description="do nested sampling on a Lennard Jones cluster")
parser.add_argument("natoms", type=int, help="number of atoms")
parser.add_argument("-K", "--nreplicas", type=int, help="number of replicas", default=300)
parser.add_argument("-n", "--mciter", type=int, default=1000, help="number of steps in the monte carlo walk")
parser.add_argument("-P", "--nproc", type=int, help="number of processors", default=1)
parser.add_argument("-q", action="store_true", help="turn off verbose printing of information at every step")
parser.add_argument("--radius", type=float, default=2.5, help="maintain atoms in a sphere of this radius")
parser.add_argument("--iprint", type=int, default=1, help="if verbose, status messages will be printed every iprint steps")
parser.add_argument("--sens-exact", action="store_true", help="use the exact version of superposition enhanced nested sampling")
parser.add_argument("--db", type=str, help="location of the database", default="")
parser.add_argument("--nminima", type=int, default=-1, help="number of minima from the database to use. If negative, use all minima")
args = parser.parse_args()
print args
if args.sens_exact and args.db == "":
raise Exception("for sens you must specify a database file")
system = LJClusterSENS(args.natoms, args.radius)
energy_accuracy = 1e-3
if args.sens_exact:
database = system.create_database(args.db, createdb=False)
if args.nminima <= 0 or args.nminima > database.number_of_minima():
minima = database.minima()
else:
minima = database.minima()[:args.nminima]
mcrunner = system.get_mc_walker(args.mciter)
nskwargs = dict(nproc=args.nproc,
verbose=not args.q, iprint=args.iprint)
print "mciter", args.mciter
if args.sens_exact:
ns = NestedSamplingSAExact(system, args.nreplicas, mcrunner,
minima, energy_accuracy,
mindist=system.get_mindist(niter=1),
minimizer=system.get_minimizer(tol=1e-4),
**nskwargs)
else:
ns = NestedSampling(system, args.nreplicas, mcrunner,
**nskwargs)
run_nested_sampling(ns, label="lj"+str(args.natoms), etol=1e-2)
