def setup_aatopology(self):
water_sites, ref = water(self.xyzfile)
rbsystem = RBTopology()
rbsystem.add_sites(water_sites)
rbsystem.finalize_setup()
#print len(rbsystem.sites), len(rbsystem.indices)
print "I have %d water molecules in the system" % len(rbsystem.sites)
rbcoords = rbsystem.coords_adapter(np.zeros(len(rbsystem.sites)*6))
for site, com in zip(rbsystem.sites, rbcoords.posRigid):
com[:] = ref.coords[site.atom_indices[0]] - site.atom_positions[0]
pot = LJ(eps=0.1550, sig=3.1536)
# get the flattened coordinate array
print "The initial energy is", pot.getEnergy(ref.coords.flatten())
rbpot = rigidbody.RBPotentialWrapper(rbsystem, pot)
print "rbpot.getEnergy(rbcoords.coords)", rbpot.getEnergy(rbcoords.coords)
e, g = rbpot.getEnergyGradient(rbcoords.coords)
g_n = rbpot.NumericalDerivative(rbcoords.coords, eps=1e-4)
cg = rbsystem.coords_adapter(g-g_n)
# coords = rbpot.getCoords()
# nrigid = rbcoords.size / 6
# print "nrigid", nrigid
self.potential = rbpot
self.nrigid = len(rbsystem.sites)
self.render_scale = 0.3
self.atom_types = rbsystem.get_atomtypes()
class TestAAMeasure(unittest.TestCase):
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites(
[create_tetrahedron() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.measure = MeasureAngleAxisCluster(self.topology)
def test_cpp_align(self):
x1 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
x2 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
x1_cpp = x1.copy()
x2_cpp = x2.copy()
x1_python = x1.copy()
x2_python = x2.copy()
ret = self.measure._align_pythonic(x1_python, x2_python)
self.assertIsNone(ret)
ret = self.measure.align(x1_cpp, x2_cpp)
self.assertIsNone(ret)
assert_arrays_almost_equal(self, x1_python, x1)
assert_arrays_almost_equal(self, x1_cpp, x1)
# assert that the center of mass coordinates didn't change
assert_arrays_almost_equal(self, x2_python[:3 * self.nrigid],
x2[:3 * self.nrigid])
assert_arrays_almost_equal(self, x2_cpp[:3 * self.nrigid],
x2[:3 * self.nrigid])
# assert that x2 actually changed
max_change = np.max(np.abs(x2_cpp - x2))
self.assertGreater(max_change, 1e-3)
assert_arrays_almost_equal(self, x2_python, x2_cpp)
def test_align_bad_input(self):
x1 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
x2 = list(x1)
with self.assertRaises(TypeError):
self.measure.align(x1, x2)
def test_symmetries(self):
tet = create_tetrahedron()
print(tet.symmetries)
self.assertEqual(len(tet.symmetries), 12)
def test_align_exact(self):
x1 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
x2 = x1.copy()
tet = create_tetrahedron()
mx = tet.symmetries[2].copy()
p = x2[-3:].copy()
x2[-3:] = rotations.rotate_aa(rotations.mx2aa(mx), p)
self.measure._align_pythonic(x1, x2)
assert_arrays_almost_equal(self, x1, x2)
class TestAAMeasure(unittest.TestCase):
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_tetrahedron() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.measure = MeasureAngleAxisCluster(self.topology)
def test_cpp_align(self):
x1 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
x2 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
x1_cpp = x1.copy()
x2_cpp = x2.copy()
x1_python = x1.copy()
x2_python = x2.copy()
ret = self.measure._align_pythonic(x1_python, x2_python)
self.assertIsNone(ret)
ret = self.measure.align(x1_cpp, x2_cpp)
self.assertIsNone(ret)
assert_arrays_almost_equal(self, x1_python, x1)
assert_arrays_almost_equal(self, x1_cpp, x1)
# assert that the center of mass coordinates didn't change
assert_arrays_almost_equal(self, x2_python[:3*self.nrigid], x2[:3*self.nrigid])
assert_arrays_almost_equal(self, x2_cpp[:3*self.nrigid], x2[:3*self.nrigid])
# assert that x2 actually changed
max_change = np.max(np.abs(x2_cpp - x2))
self.assertGreater(max_change, 1e-3)
assert_arrays_almost_equal(self, x2_python, x2_cpp)
def test_align_bad_input(self):
x1 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
x2 = list(x1)
with self.assertRaises(TypeError):
self.measure.align(x1, x2)
def test_symmetries(self):
tet = create_tetrahedron()
print(tet.symmetries)
self.assertEqual(len(tet.symmetries), 12)
def test_align_exact(self):
x1 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
x2 = x1.copy()
tet = create_tetrahedron()
mx = tet.symmetries[2].copy()
p = x2[-3:].copy()
x2[-3:] = rotations.rotate_aa(rotations.mx2aa(mx), p)
self.measure._align_pythonic(x1, x2)
assert_arrays_almost_equal(self, x1, x2)
def make_atom_indices_cpp_topology(self, atom_indices=None):
sites = [make_otp() for _ in xrange(self.nrigid)]
if atom_indices is None:
atom_indices = np.array(range(self.nrigid * 3), dtype=int)
np.random.shuffle(atom_indices)
i = 0
for site in sites:
site.atom_indices = atom_indices[i:i + site.get_natoms()].copy()
i += site.get_natoms()
topology = RBTopology()
topology.add_sites(sites)
topology.finalize_setup(use_cpp=False)
return topology, atom_indices
def make_atom_indices_cpp_topology(self, atom_indices=None):
sites = [make_otp() for _ in xrange(self.nrigid)]
if atom_indices is None:
atom_indices = np.array(range(self.nrigid*3), dtype=int)
np.random.shuffle(atom_indices)
i = 0
for site in sites:
site.atom_indices = atom_indices[i:i+site.get_natoms()].copy()
i += site.get_natoms()
topology = RBTopology()
topology.add_sites(sites)
topology.finalize_setup(use_cpp=False)
return topology, atom_indices
def setup_aatopology(self):
"""this sets up the topology for the whole rigid body system"""
topology = RBTopology()
topology.add_sites([self.make_otp() for _ in xrange(self.nrigid)])
self.render_scale = 0.2
self.atom_types = topology.get_atomtypes()
self.draw_bonds = []
for i in xrange(self.nrigid):
self.draw_bonds.append((3*i, 3*i+1))
self.draw_bonds.append((3*i, 3*i+2))
topology.finalize_setup()
return topology
class TestAAMindist(unittest.TestCase):
def setUp(self):
#GMIN.initialize()
# self.pot = GMINPotential(GMIN)
self.nrigid = 10
self.water = create_water()
self.topology = RBTopology()
self.topology.add_sites(
[deepcopy(self.water) for _ in range(self.nrigid)])
self.topology.finalize_setup()
# def test_zeroev(self):
# x = self.pot.getCoords()
# zev = self.topology.zeroEV(x)
#
# eps = 1e-5
# for dx in zev:
# print "ev test", (self.pot.getEnergy(x) - self.pot.getEnergy(x + eps*dx))/eps
#
# dx = np.random.random(x.shape)
# dx/=np.linalg.norm(dx)
# print "ev test", (self.pot.getEnergy(x) - self.pot.getEnergy(x + eps*dx))/eps
def test_distance(self):
for i in range(100):
coords1 = np.random.random(6 * self.nrigid) * 4
coords2 = np.random.random(6 * self.nrigid) * 4
coords1[:3 * self.nrigid] = 0
coords2[:3 * self.nrigid] = 0
measure1 = am.MeasureAngleAxisCluster(self.topology)
measure2 = am.MeasureRigidBodyCluster(self.topology)
#print
self.assertAlmostEqual(measure1.get_dist(coords1, coords2),
measure2.get_dist(coords1, coords2))
class TestAATransform(unittest.TestCase):
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_water() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.transform = TransformAngleAxisCluster(self.topology)
def test_cpp_rotate(self):
x0 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
aa = random_aa()
mx = aa2mx(aa)
x0_rotated = x0.copy()
self.transform.rotate(x0_rotated, mx)
x0_rotated_python = x0.copy()
self.transform._rotate_python(x0_rotated_python, mx)
assert_arrays_almost_equal(self, x0_rotated, x0_rotated_python)
mx_reverse = aa2mx(-aa)
self.transform.rotate(x0_rotated, mx_reverse)
assert_arrays_almost_equal(self, x0, x0_rotated)
class TestAAMindist(unittest.TestCase):
def setUp(self):
#GMIN.initialize()
# self.pot = GMINPotential(GMIN)
self.nrigid = 10
self.water = create_water()
self.topology = RBTopology()
self.topology.add_sites([deepcopy(self.water) for _ in range(self.nrigid)])
self.topology.finalize_setup()
# def test_zeroev(self):
# x = self.pot.getCoords()
# zev = self.topology.zeroEV(x)
#
# eps = 1e-5
# for dx in zev:
# print "ev test", (self.pot.getEnergy(x) - self.pot.getEnergy(x + eps*dx))/eps
#
# dx = np.random.random(x.shape)
# dx/=np.linalg.norm(dx)
# print "ev test", (self.pot.getEnergy(x) - self.pot.getEnergy(x + eps*dx))/eps
def test_distance(self):
for i in range(100):
coords1 = np.random.random(6*self.nrigid)*4
coords2 = np.random.random(6*self.nrigid)*4
coords1[:3*self.nrigid]=0
coords2[:3*self.nrigid]=0
measure1 = am.MeasureAngleAxisCluster(self.topology)
measure2 = am.MeasureRigidBodyCluster(self.topology)
#print
self.assertAlmostEqual(measure1.get_dist(coords1, coords2),
measure2.get_dist(coords1, coords2))
class TestAATransform(unittest.TestCase):
def setUp(self):
self.nrigid = 10
self.topology = RBTopology()
self.topology.add_sites([create_water() for _ in range(self.nrigid)])
self.topology.finalize_setup()
self.transform = TransformAngleAxisCluster(self.topology)
def test_cpp_rotate(self):
x0 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
aa = random_aa()
mx = aa2mx(aa)
x0_rotated = x0.copy()
self.transform.rotate(x0_rotated, mx)
x0_rotated_python = x0.copy()
self.transform._rotate_python(x0_rotated_python, mx)
assert_arrays_almost_equal(self, x0_rotated, x0_rotated_python)
mx_reverse = aa2mx(-aa)
self.transform.rotate(x0_rotated, mx_reverse)
assert_arrays_almost_equal(self, x0, x0_rotated)
class TestOTPExplicit(unittest.TestCase):
def setUp(self):
nrigid = 3
self.topology = RBTopology()
self.topology.add_sites([make_otp() for i in range(nrigid)])
self.topology.finalize_setup()
cartesian_potential = LJ()
self.pot = RBPotentialWrapper(self.topology, cartesian_potential)
self.x0 = _x03
self.x0 = np.array(self.x0)
self.e0 = -17.3387670023
assert nrigid * 6 == self.x0.size
self.x0atomistic = _x03_atomistic
self.nrigid = nrigid
def test_energy(self):
e = self.pot.getEnergy(self.x0)
self.assertAlmostEqual(e, self.e0, delta=1e-4)
def test_energy_gradient(self):
e = self.pot.getEnergy(self.x0)
gnum = self.pot.NumericalDerivative(self.x0)
e2, g = self.pot.getEnergyGradient(self.x0)
self.assertAlmostEqual(e, e2, delta=1e-4)
for i in range(g.size):
self.assertAlmostEqual(g[i], gnum[i], 2)
def test_to_atomistic(self):
xatom = self.topology.to_atomistic(self.x0).flatten()
for i in range(xatom.size):
self.assertAlmostEqual(xatom[i], self.x0atomistic[i], 2)
def test_site_to_atomistic(self):
rf = make_otp()
p = np.array([1., 2, 3])
p /= np.linalg.norm(p)
com = np.array([4., 5, 6])
print("otp to atomistic")
print(rf.to_atomistic(com, p))
print("otp transform grad")
g = np.array(list(range(9)), dtype=float).reshape([-1, 3])
print(g.reshape(-1))
print(rf.transform_grad(p, g))
def test_to_atomistic2(self):
x0 = np.array(list(range(self.nrigid * 6)), dtype=float)
x2 = x0.reshape([-1, 3])
for p in x2[self.nrigid:, :]:
p /= np.linalg.norm(p)
atomistic = self.topology.to_atomistic(x0).flatten()
from pele.potentials import LJ
lj = LJ()
e, g = lj.getEnergyGradient(atomistic.reshape(-1))
grb = self.topology.transform_gradient(x0, g)
rbpot = RBPotentialWrapper(self.topology, lj)
print(rbpot.getEnergy(x0))
class TestOTPExplicit(unittest.TestCase):
def make_otp(self):
"""this constructs a single OTP molecule"""
otp = RigidFragment()
otp.add_atom("O", np.array([0.0, -2. / 3 * np.sin(7. * pi / 24.),
0.0]), 1.)
otp.add_atom(
"O",
np.array([cos(7. * pi / 24.), 1. / 3. * sin(7. * pi / 24.), 0.0]),
1.)
otp.add_atom(
"O",
np.array([-cos(7. * pi / 24.), 1. / 3. * sin(7. * pi / 24), 0.0]),
1.)
otp.finalize_setup()
return otp
def setUp(self):
nrigid = 3
self.topology = RBTopology()
self.topology.add_sites([self.make_otp() for i in xrange(nrigid)])
self.topology.finalize_setup()
cartesian_potential = LJ()
self.pot = RBPotentialWrapper(self.topology, cartesian_potential)
self.x0 = _x03
self.x0 = np.array(self.x0)
self.e0 = -17.3387670023
assert nrigid * 6 == self.x0.size
self.x0atomistic = _x03_atomistic
self.nrigid = nrigid
def test_energy(self):
e = self.pot.getEnergy(self.x0)
self.assertAlmostEqual(e, self.e0, delta=1e-4)
def test_energy_gradient(self):
e = self.pot.getEnergy(self.x0)
gnum = self.pot.NumericalDerivative(self.x0)
e2, g = self.pot.getEnergyGradient(self.x0)
self.assertAlmostEqual(e, e2, delta=1e-4)
for i in xrange(g.size):
self.assertAlmostEqual(g[i], gnum[i], 2)
def test_to_atomistic(self):
xatom = self.topology.to_atomistic(self.x0).flatten()
for i in xrange(xatom.size):
self.assertAlmostEqual(xatom[i], self.x0atomistic[i], 2)
def test_site_to_atomistic(self):
rf = self.make_otp()
p = np.array([1., 2, 3])
p /= np.linalg.norm(p)
com = np.array([4., 5, 6])
print "otp to atomistic"
print rf.to_atomistic(com, p)
print "otp transform grad"
g = np.array(range(9), dtype=float).reshape([-1, 3])
print g.reshape(-1)
print rf.transform_grad(p, g)
def test_to_atomistic2(self):
x0 = np.array(range(self.nrigid * 6), dtype=float)
x2 = x0.reshape([-1, 3])
for p in x2[self.nrigid:, :]:
p /= np.linalg.norm(p)
atomistic = self.topology.to_atomistic(x0).flatten()
from pele.potentials import LJ
lj = LJ()
e, g = lj.getEnergyGradient(atomistic.reshape(-1))
grb = self.topology.transform_gradient(x0, g)
rbpot = RBPotentialWrapper(self.topology, lj)
print rbpot.getEnergy(x0)
def make_normal_cpp_topology(self):
sites = [make_otp() for _ in xrange(self.nrigid)]
normal_topology = RBTopology()
normal_topology.add_sites(sites)
normal_topology.finalize_setup()
return normal_topology
class TestOTPExplicit(unittest.TestCase):
def setUp(self):
nrigid = 3
self.topology = RBTopology()
self.topology.add_sites([make_otp() for i in range(nrigid)])
self.topology.finalize_setup()
cartesian_potential = LJ()
self.pot = RBPotentialWrapper(self.topology, cartesian_potential)
self.x0 = _x03
self.x0 = np.array(self.x0)
self.e0 = -17.3387670023
assert nrigid * 6 == self.x0.size
self.x0atomistic = _x03_atomistic
self.nrigid = nrigid
def test_energy(self):
e = self.pot.getEnergy(self.x0)
self.assertAlmostEqual(e, self.e0, delta=1e-4)
def test_energy_gradient(self):
e = self.pot.getEnergy(self.x0)
gnum = self.pot.NumericalDerivative(self.x0)
e2, g = self.pot.getEnergyGradient(self.x0)
self.assertAlmostEqual(e, e2, delta=1e-4)
for i in range(g.size):
self.assertAlmostEqual(g[i], gnum[i], 2)
def test_to_atomistic(self):
xatom = self.topology.to_atomistic(self.x0).flatten()
for i in range(xatom.size):
self.assertAlmostEqual(xatom[i], self.x0atomistic[i], 2)
def test_site_to_atomistic(self):
rf = make_otp()
p = np.array([1., 2, 3])
p /= np.linalg.norm(p)
com = np.array([4., 5, 6])
print("otp to atomistic")
print(rf.to_atomistic(com, p))
print("otp transform grad")
g = np.array(list(range(9)), dtype=float).reshape([-1,3])
print(g.reshape(-1))
print(rf.transform_grad(p, g))
def test_to_atomistic2(self):
x0 = np.array(list(range(self.nrigid * 6)), dtype=float)
x2 = x0.reshape([-1,3])
for p in x2[self.nrigid:,:]:
p /= np.linalg.norm(p)
atomistic = self.topology.to_atomistic(x0).flatten()
from pele.potentials import LJ
lj = LJ()
e, g = lj.getEnergyGradient(atomistic.reshape(-1))
grb = self.topology.transform_gradient(x0, g)
rbpot = RBPotentialWrapper(self.topology, lj)
print(rbpot.getEnergy(x0))
class TestOTPExplicit(unittest.TestCase):
def make_otp(self):
"""this constructs a single OTP molecule"""
otp = RigidFragment()
otp.add_atom("O", np.array([0.0, -2./3 * np.sin( 7.*pi/24.), 0.0]), 1.)
otp.add_atom("O", np.array([cos( 7.*pi/24.), 1./3. * sin( 7.* pi/24.), 0.0]), 1.)
otp.add_atom("O", np.array([-cos( 7.* pi/24.), 1./3. * sin( 7.*pi/24), 0.0]), 1.)
otp.finalize_setup()
return otp
def setUp(self):
nrigid = 3
self.topology = RBTopology()
self.topology.add_sites([self.make_otp() for i in xrange(nrigid)])
self.topology.finalize_setup()
cartesian_potential = LJ()
self.pot = RBPotentialWrapper(self.topology, cartesian_potential)
self.x0 = _x03
self.x0 = np.array(self.x0)
self.e0 = -17.3387670023
assert nrigid * 6 == self.x0.size
self.x0atomistic = _x03_atomistic
self.nrigid = nrigid
def test_energy(self):
e = self.pot.getEnergy(self.x0)
self.assertAlmostEqual(e, self.e0, delta=1e-4)
def test_energy_gradient(self):
e = self.pot.getEnergy(self.x0)
gnum = self.pot.NumericalDerivative(self.x0)
e2, g = self.pot.getEnergyGradient(self.x0)
self.assertAlmostEqual(e, e2, delta=1e-4)
for i in xrange(g.size):
self.assertAlmostEqual(g[i], gnum[i], 2)
def test_to_atomistic(self):
xatom = self.topology.to_atomistic(self.x0).flatten()
for i in xrange(xatom.size):
self.assertAlmostEqual(xatom[i], self.x0atomistic[i], 2)
def test_site_to_atomistic(self):
rf = self.make_otp()
p = np.array([1., 2, 3])
p /= np.linalg.norm(p)
com = np.array([4., 5, 6])
print "otp to atomistic"
print rf.to_atomistic(com, p)
print "otp transform grad"
g = np.array(range(9), dtype=float).reshape([-1,3])
print g.reshape(-1)
print rf.transform_grad(p, g)
def test_to_atomistic2(self):
x0 = np.array(range(self.nrigid * 6), dtype=float)
x2 = x0.reshape([-1,3])
for p in x2[self.nrigid:,:]:
p /= np.linalg.norm(p)
atomistic = self.topology.to_atomistic(x0).flatten()
from pele.potentials import LJ
lj = LJ()
e, g = lj.getEnergyGradient(atomistic.reshape(-1))
grb = self.topology.transform_gradient(x0, g)
rbpot = RBPotentialWrapper(self.topology, lj)
print rbpot.getEnergy(x0)
def make_normal_cpp_topology(self):
sites = [make_otp() for _ in xrange(self.nrigid)]
normal_topology = RBTopology()
normal_topology.add_sites(sites)
normal_topology.finalize_setup()
return normal_topology
