def test_site_distance_squared(self):
print("\ntest site distance squared")
c0 = np.zeros(3)
c1 = np.ones(3)
p0 = self.p0.copy()
p1 = p0 + 1
site = make_otp()
d2 = site.distance_squared(c0, p0, c1, p1)
d2p = _sitedist(c1 - c0, p0, p1, site.S, site.W, site.cog)
self.assertAlmostEqual(d2, 10.9548367929, 5)
def test_site_distance_squared(self):
print("\ntest site distance squared")
c0 = np.zeros(3)
c1 = np.ones(3)
p0 = self.p0.copy()
p1 = p0 + 1
site = make_otp()
d2 = site.distance_squared(c0, p0, c1, p1)
d2p = _sitedist(c1-c0, p0, p1, site.S, site.W, site.cog)
self.assertAlmostEqual(d2, 10.9548367929, 5)
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 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 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 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(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 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 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
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
