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("db", type=str, help="location of the database")
parser.add_argument("--normalmodes", type=str, help="store the full normalmodes as well")
args = parser.parse_args()
system = LJCluster(args.natoms,)
if False:
# build the database
database = system.create_database(args.db, createdb=True)
bh = system.get_basinhopping(database)
bh.run(1000)
else:
database = system.create_database(args.db, createdb=False)
assert database.number_of_minima() > 0
print "computing the vibrational free energy and the point group order"
get_thermodynamic_information(system, database)
print "computing the normal modes"
get_all_normalmodes(system, database)
def setUp1(self, nproc=1):
self.set_up_system()
self.nreplicas = 10
self.stepsize = 0.01
self.nproc = nproc
self.database = self.system.create_database()
# add some minima to the database
bh = self.system.get_basinhopping(self.database, outstream=None)
while self.database.number_of_minima() < 2:
bh.run(1)
# compute the thermodynamic information
get_thermodynamic_information(self.system, self.database)
get_all_normalmodes(self.system, self.database)
self.minima = list(self.database.minima())
assert self.database.number_of_minima() > 1, "%d minima" % self.database.number_of_minima()
self.mc_runner = self.system.get_mc_walker(mciter=200)
self.energy_accuracy = 1e-4
self.ns = NestedSamplingSAExact(self.system, self.nreplicas, self.mc_runner,
self.minima, self.energy_accuracy,
mindist=self.system.get_mindist(),
config_tests = self.system.get_config_tests(),
stepsize=0.1, nproc=nproc, verbose=True, iprint=100)
self.Emax0 = self.ns.replicas[-1].energy
self.run_ns(max_iter=1000, Etol=.001)
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("db", type=str, help="location of the database")
parser.add_argument("--normalmodes",
type=str,
help="store the full normalmodes as well")
args = parser.parse_args()
system = LJCluster(args.natoms, )
if False:
# build the database
database = system.create_database(args.db, createdb=True)
bh = system.get_basinhopping(database)
bh.run(1000)
else:
database = system.create_database(args.db, createdb=False)
assert database.number_of_minima() > 0
print "computing the vibrational free energy and the point group order"
get_thermodynamic_information(system, database)
print "computing the normal modes"
get_all_normalmodes(system, database)
def setUp(self):
self.natoms = 6
self.system = LJCluster(self.natoms)
# create a database
self.database = self.system.create_database()
# add some minima to the database
bh = self.system.get_basinhopping(self.database, outstream=None)
while self.database.number_of_minima() < 2:
bh.run(1)
get_thermodynamic_information(self.system, self.database)
get_all_normalmodes(self.system, self.database)
self.ndof = self.natoms * 3 - 6
self.sampler = SASampler(self.database.minima(), self.ndof)
def setUp(self):
self.natoms = 6
self.system = LJCluster(self.natoms)
# create a database
self.database = self.system.create_database()
# add some minima to the database
bh = self.system.get_basinhopping(self.database, outstream=None)
while self.database.number_of_minima() < 2:
bh.run(1)
get_thermodynamic_information(self.system, self.database)
get_all_normalmodes(self.system, self.database)
self.ndof = self.natoms * 3 - 6
self.sampler = SASampler(self.database.minima(), self.ndof)
def build_database(system, nminima, dbfname=None, maxiter=1000):
if dbfname is None:
db = system.create_database()
else:
db = system.create_database(dbfname)
bh = system.get_basinhopping(db, outstream=None)
i = 0
while db.number_of_minima() < nminima:
bh.run(1)
i += 1
if i >= maxiter:
break
get_thermodynamic_information(system, db)
get_all_normalmodes(system, db)
return db
def setUp1(self, nproc=1):
self.set_up_system()
self.nreplicas = 10# * nproc
self.stepsize = 0.01
self.nproc = nproc
self.database = self.system.create_database()
# add some minima to the database
bh = self.system.get_basinhopping(self.database, outstream=None)
while self.database.number_of_minima() < 2:
bh.run(1)
# compute the thermodynamic information
get_thermodynamic_information(self.system, self.database)
get_all_normalmodes(self.system, self.database)
self.minima = list(self.database.minima())
assert self.database.number_of_minima() > 1, "%d minima" % self.database.number_of_minima()
self.mc_runner = self.system.get_mc_walker(mciter=200)
self.energy_accuracy = 1e-4
self.hsa_sampler = HSASamplerCluster(self.minima, self.system.k, copy_minima=True,
center_minima=True,
energy_accuracy=self.energy_accuracy,
compare_structures=self.system.get_compare_exact(),
mindist=self.system.get_mindist(),
minimizer=self.system.get_minimizer(),
debug=True)
replicas = _utils.create_replicas(self.system, self.nreplicas)
potential = self.system.get_potential()
potential.get_energy = potential.getEnergy
self.ns = NestedSamplingSAExact(replicas, self.mc_runner,
self.hsa_sampler, potential,
config_tests=self.system.get_config_tests(),
nproc=nproc, verbose=True, iprint=1, debug=True)
self.Emax0 = self.ns.replicas[-1].energy
self.run_ns(max_iter=1000, Etol=.001)
def setUp1(self, nproc=1):
self.set_up_system()
self.nreplicas = 10
self.stepsize = 0.01
self.nproc = nproc
self.database = self.system.create_database()
# add some minima to the database
bh = self.system.get_basinhopping(self.database, outstream=None)
while self.database.number_of_minima() < 2:
bh.run(1)
# compute the thermodynamic information
get_thermodynamic_information(self.system, self.database)
get_all_normalmodes(self.system, self.database)
self.minima = list(self.database.minima())
assert self.database.number_of_minima(
) > 1, "%d minima" % self.database.number_of_minima()
self.mc_runner = self.system.get_mc_walker(mciter=200)
self.energy_accuracy = 1e-4
self.ns = NestedSamplingSAExact(
self.system,
self.nreplicas,
self.mc_runner,
self.minima,
self.energy_accuracy,
mindist=self.system.get_mindist(),
config_tests=self.system.get_config_tests(),
stepsize=0.1,
nproc=nproc,
verbose=True,
iprint=100)
self.Emax0 = self.ns.replicas[-1].energy
self.run_ns(max_iter=1000, Etol=.001)
def setUp(self):
super(TestGetNormalModes, self).setUp()
get_all_normalmodes(self.system, self.database)
