class TestMinimaSearch(unittest.TestCase):
def setUp(self):
self.natoms = 6
self.system = LJClusterSENS(self.natoms, 2.5)
# 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)
self.ndof = self.natoms * 3 - 6
self.minima_searcher = _MinimaSearcher(self.database.minima(), energy_accuracy=1e-4, compare_structures=self.system.get_compare_exact())
def test_exact(self):
for m in self.database.minima():
mret, tform = self.minima_searcher.get_minima(m.energy, m.coords)
self.assertEqual(m, mret)
def test_random(self):
for m in self.database.minima():
mret, tform = self.minima_searcher.get_minima(m.energy + np.random.uniform(-1e-4, 1e-4), m.coords)
self.assertEqual(m, mret)
def test_none(self):
for m in self.database.minima():
mret, tform = self.minima_searcher.get_minima(m.energy + 10., m.coords)
self.assertIsNone(mret)
class TestSENSExact_LJ(_test_ns_lj.TestNS_LJ):
def setUp(self):
# self.seed = 4
# np.random.seed(self.seed)
self.setUp1()
def set_up_system(self):
self.natoms = 6
self.gmin = -12.7121
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.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 test1(self):
super(TestSENSExact_LJ, self).test1()
self.assertGreater(self.ns.count_sampled_minima, 0)
class TestSENSExact_LJ(_test_ns_lj.TestNS_LJ):
def setUp(self):
# self.seed = 4
# np.random.seed(self.seed)
self.setUp1()
def set_up_system(self):
self.natoms = 6
self.gmin = -12.7121
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.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 test1(self):
super(TestSENSExact_LJ, self).test1()
self.assertGreater(self.ns.count_sampled_minima, 0)
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)
class TestMinimaSearch(unittest.TestCase):
def setUp(self):
self.natoms = 6
self.system = LJClusterSENS(self.natoms, 2.5)
# 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)
self.ndof = self.natoms * 3 - 6
self.minima_searcher = _MinimaSearcher(
self.database.minima(),
energy_accuracy=1e-4,
compare_structures=self.system.get_compare_exact())
def test_exact(self):
for m in self.database.minima():
mret, tform = self.minima_searcher.get_minima(m.energy, m.coords)
self.assertEqual(m, mret)
def test_random(self):
for m in self.database.minima():
mret, tform = self.minima_searcher.get_minima(
m.energy + np.random.uniform(-1e-4, 1e-4), m.coords)
self.assertEqual(m, mret)
def test_none(self):
for m in self.database.minima():
mret, tform = self.minima_searcher.get_minima(
m.energy + 10., m.coords)
self.assertIsNone(mret)
class TestSENSExact_LJ(unittest.TestCase):
def setUp(self):
self.seed = np.random.randint(1000000)
# self.seed = 549670 # failed self.assertGreater(self.ns.count_sampled_minima, 0)
print "seed", self.seed
np.random.seed(self.seed)
self.setUp1()
def setUp1(self, nproc=1):
self.natoms = 31
self.system = LJClusterSENS(self.natoms, 2.5)
self.ndof = 3*self.natoms - 6
self.nreplicas = 10
self.stepsize = 0.01
self.nproc = nproc
try:
self.database = self.system.create_database("/scratch/scratch2/js850/sens/testruns/lj31/lj31.sqlite", createdb=False)
except IOError:
self.database = build_database(self.system, 4)
self.minima = list(self.database.minima())
assert self.database.number_of_minima() > 1, "%d minima" % self.database.number_of_minima()
self.sampler = HSASamplerCluster(self.minima, self.ndof, copy_minima=True,
center_minima=True,
compare_structures=self.system.get_compare_exact(),
mindist=self.system.get_mindist(),
minimizer=self.system.get_minimizer())
self.Emax = min((m.energy for m in self.minima)) + 1.
# for performing transformations like rotations, translations, permutations, etc
self.transform = TransformAtomicCluster()
# this is a list of random transformations that don't change the energy
self.transformations = [self.rtrans, self.rrot, self.invert, self.rperm]
def rtrans(self, x):
vec3 = np.random.uniform(-1,1,3)
self.transform.translate(x, vec3)
def rrot(self, x):
q = rotations.random_q()
mx = rotations.q2mx(q)
self.transform.rotate(x, mx)
def invert(self, x):
self.transform.invert(x)
def rperm(self, x):
perm = range(self.natoms)
np.random.shuffle(perm)
self.transform.permute(x, perm)
def do_test(self, tform):
# sample a configurations fr
# sample a configuration from the HSA
m, xsampled = self.sampler.sample_coords(self.Emax)
# get the energy of that configuration in the HSA
E_HSA = self.sampler.compute_energy(xsampled, m)
# get the real energy of the sampled configuration
pot = self.system.get_potential()
Esampled = pot.getEnergy(xsampled)
r = Replica(xsampled, Esampled)
# transform xsampled in a way that preserves the real energy but not necessarily the HSA energy
tform(xsampled)
# assert the real energy has not changed
Etrans = pot.getEnergy(xsampled)
self.assertAlmostEqual(r.energy, Etrans, delta=1e-4)
# use the nested sampling routine to compute the HSA energy of xsampled.
# This should undo the transformations we applied and find the correct HSA energy
m_quench, E_HSA_computed = self.sampler.compute_energy_in_HSA(r.energy, r.x)
# assert that self.ns._compute_energy_in_SA(r) was able to recover the correct HSA energy
self.assertIsNotNone(E_HSA_computed)
self.assertAlmostEqual(E_HSA, E_HSA_computed, delta=1e-4)
self.assertAlmostEqual(m.energy, m_quench.energy, delta=1e-4)
def fchain(self, flist):
"""return a function which applies all of the functions in flist to the input"""
def function_chain(x):
for f in reversed(flist):
f(x)
return function_chain
def test1(self):
"""run do_test() on all combinations transformations"""
for f in self.transformations:
self.do_test(f)
def test_2(self):
"""run do_test() on all combinations of length 2 of the transformations
"""
for flist in itertools.product(self.transformations, repeat=2):
tform = self.fchain(flist)
self.do_test(tform)
def test_10(self):
"""run do_test() on all combinations of length 10 of the transformations
"""
maxiter = 500
i = 0
for flist in itertools.product(self.transformations, repeat=10):
tform = self.fchain(flist)
self.do_test(tform)
i += 1
if i >= maxiter: break
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("--sens-approximate", action="store_true", help="use the approximate version of superposition enhanced nested sampling")
parser.add_argument("--minprob", type=float, default=1., help="only for sens-approximate: probability of sampling from the database (by default <minprob>/K),"
"default value 1")
parser.add_argument("--energy-offset", type=float, default=2.5, help="only for sens-approximate: value of Emax where the probabilty"
"starts to become non zero is <energy_max_database> + <energy_offset>")
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")
parser.add_argument("--energy-onset", type=float, help="energy at which start sampling from database, by default maximum energy in database",default=None)
parser.add_argument("--stop-crit", type=float, default=1e-3, help="run will terminate when stop_crit is larger than the difference between the maximum and minimum replica energies")
parser.add_argument("--cpfile", type=str, help="checkpoint file name, unless renamed it takes default output name: <label>.replicas.p", default = None)
parser.add_argument("--cpfreq", type=int, help="checkpointing frequency in number of steps", default = 10000)
parser.add_argument("--cpstart", action="store_true", help="start calculation from checkpoint binary file")
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)
args = parser.parse_args()
print args
if (args.sens_exact or args.sens_approximate) 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 or args.sens_approximate:
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]
print "using", len(minima), "minima"
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
mcrunner = system.get_mc_walker(args.mciter)
nskwargs = dict(nproc=args.nproc, verbose=not args.q,
iprint=args.iprint, dispatcher_URI = dispatcherURI,
cpfreq = args.cpfreq, cpfile = args.cpfile,
cpstart = args.cpstart)
# create the potential object
potential = system.get_potential()
potential.get_energy = potential.getEnergy
# create the replicas
replicas = []
for i in xrange(args.nreplicas):
x = system.get_random_configuration()
e = potential.getEnergy(x)
replicas.append(Replica(x, e))
print "mciter", args.mciter
print "radius", args.radius
if args.sens_exact:
hsa_sampler = HSASamplerCluster(minima, system.k, copy_minima=True,
center_minima=True, energy_accuracy=energy_accuracy,
compare_structures=system.get_compare_exact(),
mindist=system.get_mindist(),
minimizer=system.get_minimizer(),
debug=True)
ns = NestedSamplingSAExact(replicas, mcrunner, hsa_sampler, potential,
config_tests=system.get_config_tests(),
**nskwargs)
elif args.sens_approximate:
ns = NestedSamplingSA(replicas, mcrunner, minima, system.k,
config_tests=system.get_config_tests(),
minprob=args.minprob, energy_offset=args.energy_offset,
energy_onset = args.energy_onset, copy_minima=True,
center_minima=True, **nskwargs)
else:
ns = NestedSampling(replicas, mcrunner,
**nskwargs)
run_nested_sampling(ns, label="lj"+str(args.natoms), etol=args.stop_crit, )
class TestSENSExact_LJ(_test_ns_lj.TestNS_LJ):
def setUp(self):
self.seed = np.random.randint(1000000)
# self.seed = 549670 # failed self.assertGreater(self.ns.count_sampled_minima, 0)
print "seed", self.seed
np.random.seed(self.seed)
self.setUp1()
def set_up_system(self):
self.natoms = 6
self.gmin = -12.7121
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# * 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 test1(self):
super(TestSENSExact_LJ, self).test1()
self.assertGreater(self.ns.number_swaps_accepted(), 0)