class TestBuildDatabase(unittest.TestCase):
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 test(self):
# for m in self.database.minima():
# print m.energy
# print self.sampler.compute_weights(-11.7)
# for i in range(10):
# m = self.sampler.sample_minimum(-11)
# print m._id
def compute_weights(self, Emax, k):
print [m.energy for m in self.database.minima()], Emax
lweights = [ - np.log(m.pgorder) + 0.5 * k * np.log(Emax - m.energy) - 0.5 * m.fvib
for m in self.database.minima() if m.energy < Emax]
lweights = np.array(lweights)
if lweights.size <= 1: return lweights
lwmax = lweights.max()
lweights -= lwmax
return np.exp(lweights)
def test1(self):
Emax = -11.7
minima, weights = self.sampler.compute_weights(0.)
minima, weights = self.sampler.compute_weights(Emax)
self.assertAlmostEqual(weights[0], 0.81256984, 3)
self.assertAlmostEqual(weights[1], 1., 7)
new_weights = self.compute_weights(Emax, self.ndof)
print weights
print new_weights
def test2(self):
Emax = -11.7
minima, weights = self.sampler.compute_weights(Emax)
minima, weights = self.sampler.compute_weights(Emax)
self.assertAlmostEqual(weights[0], 0.81256984, 3)
self.assertAlmostEqual(weights[1], 1., 7)
def test3(self):
m = self.sampler.sample_minimum(-11.7)
self.assertIn(m, self.database.minima())
def test4(self):
"""check that the HSA energy is computed correctly"""
pot = self.system.get_potential()
for m in self.database.minima():
x = m.coords.copy()
x += np.random.uniform(-1e-3, 1e-3, x.shape)
ehsa = self.sampler.compute_energy(x, m, x0=m.coords)
ecalc = pot.getEnergy(x)
ecompare = (ehsa - ecalc) / (ecalc - m.energy)
print ehsa - m.energy, ecalc - m.energy, m.energy, ecompare
self.assertAlmostEqual(ecompare, 0., 1)
def test_rotation(self):
"""assert that the HSA energy is *not* invariant under rotation"""
pot = self.system.get_potential()
aa = rotations.random_aa()
rmat = rotations.aa2mx(aa)
from pele.mindist import TransformAtomicCluster
tform = TransformAtomicCluster(can_invert=True)
for m in self.database.minima():
x = m.coords.copy()
# randomly move the atoms by a small amount
x += np.random.uniform(-1e-3, 1e-3, x.shape)
ehsa1 = self.sampler.compute_energy(x, m, x0=m.coords)
ecalc = pot.getEnergy(x)
# now rotate by a random matrix
xnew = x.copy()
tform.rotate(xnew, rmat)
ehsa2 = self.sampler.compute_energy(xnew, m, x0=m.coords)
ecalc2 = pot.getEnergy(xnew)
self.assertAlmostEqual(ecalc, ecalc2, 5)
self.assertNotAlmostEqual(ehsa1, ehsa2, 1)
# def test_rotation_2(self):
# """assert that the HSA energy *is* invariant under rotation *if* the initial coords are also rotated"""
# pot = self.system.get_potential()
# aa = rotations.random_aa()
# rmat = rotations.aa2mx(aa)
# from pele.mindist import TransformAtomicCluster
# tform = TransformAtomicCluster(can_invert=True)
# for m in self.database.minima():
# x = m.coords.copy()
# # randomly move the atoms by a small amount
# x += np.random.uniform(-1e-3, 1e-3, x.shape)
# ehsa1 = self.sampler.compute_energy(x, m, x0=m.coords)
# ecalc = pot.getEnergy(x)
# # now rotate by a random matrix
# xnew = x.copy()
# tform.rotate(xnew, rmat)
# xmnew = m.coords.copy()
# tform.rotate(xmnew, rmat)
# ehsa2 = self.sampler.compute_energy(xnew, m, x0=xmnew)
# ecalc2 = pot.getEnergy(xnew)
# self.assertAlmostEqual(ecalc, ecalc2, 5)
# self.assertAlmostEqual(ehsa1, ehsa2, 3)
def test_permutation(self):
"""assert that the HSA energy is not invariant under permutation"""
pot = self.system.get_potential()
perm = range(self.natoms)
np.random.shuffle(perm)
from pele.mindist import TransformAtomicCluster
tform = TransformAtomicCluster(can_invert=True)
for m in self.database.minima():
x = m.coords.copy()
# randomly move the atoms by a small amount
x += np.random.uniform(-1e-3, 1e-3, x.shape)
ehsa1 = self.sampler.compute_energy(x, m, x0=m.coords)
ecalc = pot.getEnergy(x)
# now rotate by a random matrix
xnew = x.copy()
xnew = tform.permute(xnew, perm)
ehsa2 = self.sampler.compute_energy(xnew, m, x0=m.coords)
ecalc2 = pot.getEnergy(xnew)
self.assertAlmostEqual(ecalc, ecalc2, 5)
self.assertNotAlmostEqual(ehsa1, ehsa2, 1)
class TestBuildDatabase(unittest.TestCase):
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 test(self):
# for m in self.database.minima():
# print m.energy
# print self.sampler.compute_weights(-11.7)
# for i in range(10):
# m = self.sampler.sample_minimum(-11)
# print m._id
def test1(self):
Emax = -11.7
minima, weights = self.sampler.compute_weights(0.)
minima, weights = self.sampler.compute_weights(Emax)
self.assertAlmostEqual(weights[0], 0.81256984, 3)
self.assertAlmostEqual(weights[1], 1., 7)
def test2(self):
Emax = -11.7
minima, weights = self.sampler.compute_weights(Emax)
minima, weights = self.sampler.compute_weights(Emax)
self.assertAlmostEqual(weights[0], 0.81256984, 3)
self.assertAlmostEqual(weights[1], 1., 7)
def test3(self):
m = self.sampler.sample_minimum(-11.7)
self.assertIn(m, self.database.minima())
def test4(self):
"""check that the HSA energy is computed correctly"""
pot = self.system.get_potential()
for m in self.database.minima():
x = m.coords.copy()
x += np.random.uniform(-1e-3, 1e-3, x.shape)
ehsa = self.sampler.compute_energy(x, m, x0=m.coords)
ecalc = pot.getEnergy(x)
ecompare = (ehsa - ecalc) / (ecalc - m.energy)
print ehsa - m.energy, ecalc - m.energy, m.energy, ecompare
self.assertAlmostEqual(ecompare, 0., 1)
def test_rotation(self):
"""assert that the HSA energy is *not* invariant under rotation"""
pot = self.system.get_potential()
aa = rotations.random_aa()
rmat = rotations.aa2mx(aa)
from pele.mindist import TransformAtomicCluster
tform = TransformAtomicCluster(can_invert=True)
for m in self.database.minima():
x = m.coords.copy()
# randomly move the atoms by a small amount
x += np.random.uniform(-1e-3, 1e-3, x.shape)
ehsa1 = self.sampler.compute_energy(x, m, x0=m.coords)
ecalc = pot.getEnergy(x)
# now rotate by a random matrix
xnew = x.copy()
tform.rotate(xnew, rmat)
ehsa2 = self.sampler.compute_energy(xnew, m, x0=m.coords)
ecalc2 = pot.getEnergy(xnew)
self.assertAlmostEqual(ecalc, ecalc2, 5)
self.assertNotAlmostEqual(ehsa1, ehsa2, 1)
# def test_rotation_2(self):
# """assert that the HSA energy *is* invariant under rotation *if* the initial coords are also rotated"""
# pot = self.system.get_potential()
# aa = rotations.random_aa()
# rmat = rotations.aa2mx(aa)
# from pele.mindist import TransformAtomicCluster
# tform = TransformAtomicCluster(can_invert=True)
# for m in self.database.minima():
# x = m.coords.copy()
# # randomly move the atoms by a small amount
# x += np.random.uniform(-1e-3, 1e-3, x.shape)
# ehsa1 = self.sampler.compute_energy(x, m, x0=m.coords)
# ecalc = pot.getEnergy(x)
# # now rotate by a random matrix
# xnew = x.copy()
# tform.rotate(xnew, rmat)
# xmnew = m.coords.copy()
# tform.rotate(xmnew, rmat)
# ehsa2 = self.sampler.compute_energy(xnew, m, x0=xmnew)
# ecalc2 = pot.getEnergy(xnew)
# self.assertAlmostEqual(ecalc, ecalc2, 5)
# self.assertAlmostEqual(ehsa1, ehsa2, 3)
def test_permutation(self):
"""assert that the HSA energy is not invariant under permutation"""
pot = self.system.get_potential()
perm = range(self.natoms)
np.random.shuffle(perm)
from pele.mindist import TransformAtomicCluster
tform = TransformAtomicCluster(can_invert=True)
for m in self.database.minima():
x = m.coords.copy()
# randomly move the atoms by a small amount
x += np.random.uniform(-1e-3, 1e-3, x.shape)
ehsa1 = self.sampler.compute_energy(x, m, x0=m.coords)
ecalc = pot.getEnergy(x)
# now rotate by a random matrix
xnew = x.copy()
xnew = tform.permute(xnew, perm)
ehsa2 = self.sampler.compute_energy(xnew, m, x0=m.coords)
ecalc2 = pot.getEnergy(xnew)
self.assertAlmostEqual(ecalc, ecalc2, 5)
self.assertNotAlmostEqual(ehsa1, ehsa2, 1)
