def _create_potential(self):
"""construct the potential which will compute the energy and gradient in atomistic (cartesian) coordinates
The bonded (hinged) sides interact with an attractive harmonic potential. Each atom
in the bond has a single interaction partner.
The loosly attractive sides interact with an LJ potential. These interactions are
not specific. Each atom interacts with every other one.
All atoms repel each other with a WCA potential.
"""
parser = MolAtomIndexParser(self.aatopology, self.nrigid)
# this is currently only set up for a tetrahedron
assert self.nrigid == 4
# do hinges
harmonic_atoms1 = []
harmonic_atoms2 = []
harmonic_atoms1 += parser.get_atom_indices(0, EDGE1_TYPE)
harmonic_atoms2 += parser.get_atom_indices(1, EDGE1_TYPE)
harmonic_atoms1 += parser.get_atom_indices(0, EDGE2_TYPE)
harmonic_atoms2 += parser.get_atom_indices(2, EDGE1_TYPE)
harmonic_atoms1 += parser.get_atom_indices(0, EDGE3_TYPE)
harmonic_atoms2 += parser.get_atom_indices(3, EDGE1_TYPE)
self.harmonic_atoms = np.array(harmonic_atoms1 + harmonic_atoms2, np.integer)
harmonic_atoms1 = np.array(harmonic_atoms1, dtype=np.integer).ravel()
harmonic_atoms2 = np.array(harmonic_atoms2, dtype=np.integer).ravel()
for i, j in zip(harmonic_atoms1, harmonic_atoms2):
self.draw_bonds.append((i,j))
# do attractive part
lj_atoms = []
lj_atoms += parser.get_atom_indices(1, EDGE2_TYPE)
lj_atoms += parser.get_atom_indices(1, EDGE3_TYPE)
lj_atoms += parser.get_atom_indices(2, EDGE2_TYPE)
lj_atoms += parser.get_atom_indices(2, EDGE3_TYPE)
lj_atoms += parser.get_atom_indices(3, EDGE2_TYPE)
lj_atoms += parser.get_atom_indices(3, EDGE3_TYPE)
lj_atoms = np.array(sorted(lj_atoms)).ravel()
self.lj_atoms = lj_atoms
self.extra_atoms = []
for i in range(self.nrigid):
self.extra_atoms += parser.get_atom_indices(i, OTHER_TYPE)
plate_pot = PlatePotential(harmonic_atoms1, harmonic_atoms2, lj_atoms, k=10)
# wrap it so it can be used with angle axis coordinates
pot = RBPotentialWrapper(self.aatopology.cpp_topology, plate_pot)
# self.aasystem.set_cpp_topology(self.pot.topology)
# raise Exception
return pot
def get_potential(self):
"""construct the rigid body potential"""
try:
return self.pot
except AttributeError:
# construct the potential which will compute the energy and gradient in atomistic (cartesian) coordinates
cartesian_potential = LJ()
# wrap it so it can be used with angle axis coordinates
self.pot = RBPotentialWrapper(self.aatopology.cpp_topology, cartesian_potential)
# self.aasystem.set_cpp_topology(self.pot.topology)
return self.pot
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))
def test_pot_wrapper(self):
from pele.angleaxis import _cpp_aa
from pele.potentials import LJ
rbpot_cpp = _cpp_aa.RBPotentialWrapper(self.topology, LJ())
rbpot = RBPotentialWrapper(self.topology, LJ())
self.assertAlmostEqual(rbpot_cpp.getEnergy(self.x0),
rbpot.getEnergy(self.x0), 4)
e1, grad1 = rbpot_cpp.getEnergyGradient(self.x0)
e2, grad2 = rbpot.getEnergyGradient(self.x0)
self.assertAlmostEqual(e1, e2, 4)
for g1, g2 in zip(grad1, grad2):
self.assertAlmostEqual(g1, g2, 3)
def get_potential(self):
"""construct the rigid body potential"""
try:
return self.pot
except AttributeError:
# construct the potential which will compute the energy and gradient
# in atomistic (cartesian) coordinates
# NOTE: Currently the LJCut potential only deals with cubic boxes
cartesian_potential = LJCut(rcut=self.cut, boxvec=self.boxvec)
# cartesian_potential = LJCutCellLists(rcut=self.cut, boxvec=self.boxvec)
# wrap it so it can be used with angle axis coordinates
self.pot = RBPotentialWrapper(self.aatopology.cpp_topology, cartesian_potential)
# self.aasystem.set_cpp_topology(self.pot.topology)
return self.pot
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
