def test_cpp_potential(self):
python_topology, atom_indices = self.make_atom_indices_python_topology()
cpp_topology, atom_indices = self.make_atom_indices_cpp_topology(atom_indices=atom_indices.copy())
lj = LJ()
pot_python = pythonRBPotentialWrapper(python_topology, lj)
pot_cpp = pythonRBPotentialWrapper(cpp_topology, lj)
coords = self.get_random_rbcoords()
e_python = pot_python.getEnergy(coords.copy())
e_cpp = pot_cpp.getEnergy(coords.copy())
self.assertAlmostEqual(e_python, e_cpp)
e1, g_python = pot_python.getEnergyGradient(coords.copy())
e2, g_cpp = pot_cpp.getEnergyGradient(coords.copy())
assert_arrays_almost_equal(self, g_python, g_cpp)
def test_potential(self):
topology, atom_indices = self.make_atom_indices_python_topology()
normal_topology = self.make_normal_python_topology()
lj = LJ()
pot = pythonRBPotentialWrapper(topology, lj)
pot_normal = pythonRBPotentialWrapper(normal_topology, lj)
coords = self.get_random_rbcoords()
energy_atom_indices = pot.getEnergy(coords.copy())
energy_normal = pot_normal.getEnergy(coords.copy())
self.assertAlmostEqual(energy_atom_indices, energy_normal)
e1, gei = pot.getEnergyGradient(coords.copy())
e2, gnorm = pot_normal.getEnergyGradient(coords.copy())
assert_arrays_almost_equal(self, gei, gnorm)
def test_cpp_potential(self):
python_topology, atom_indices = self.make_atom_indices_python_topology(
)
cpp_topology, atom_indices = self.make_atom_indices_cpp_topology(
atom_indices=atom_indices.copy())
lj = LJ()
pot_python = pythonRBPotentialWrapper(python_topology, lj)
pot_cpp = pythonRBPotentialWrapper(cpp_topology, lj)
coords = self.get_random_rbcoords()
e_python = pot_python.getEnergy(coords.copy())
e_cpp = pot_cpp.getEnergy(coords.copy())
self.assertAlmostEqual(e_python, e_cpp)
e1, g_python = pot_python.getEnergyGradient(coords.copy())
e2, g_cpp = pot_cpp.getEnergyGradient(coords.copy())
assert_arrays_almost_equal(self, g_python, g_cpp)
def test_potential(self):
topology, atom_indices = self.make_atom_indices_python_topology()
normal_topology = self.make_normal_python_topology()
lj = LJ()
pot = pythonRBPotentialWrapper(topology, lj)
pot_normal = pythonRBPotentialWrapper(normal_topology, lj)
coords = self.get_random_rbcoords()
energy_atom_indices = pot.getEnergy(coords.copy())
energy_normal = pot_normal.getEnergy(coords.copy())
self.assertAlmostEqual(energy_atom_indices, energy_normal)
e1, gei = pot.getEnergyGradient(coords.copy())
e2, gnorm = pot_normal.getEnergyGradient(coords.copy())
assert_arrays_almost_equal(self, gei, gnorm)