def test_partial1(self):
lx = 8
ly = 11
lz = 9
N = 10
dz = 1.1
r0 = 1.0
potential = 'Harmonic'
partial_indices = [4, 3, 5]
x = np.array([0.0] * N)
y = np.array([0.0] * N)
z = np.array([dz * i - lz / 2.0 for i in range(N)])
t = [0] * N
bonds = [[i, j] for i, j in zip(range(N - 1), range(1, N))]
U0 = 0
U0 += self.harmonic(dz, 1.0, r0) * (len(partial_indices) - 1
) #inner bonds
U0 += self.harmonic(dz, 1.0, r0) * (2) #outer bonds
NBPT = PairTable(types=['P1'],
parms=['epsilon', 'rcut', 'sigma', 'potential'])
NBPT.setUnsetValues('epsilon', 1.0)
NBPT.setUnsetValues('sigma', 1.0)
NBPT.setUnsetValues('rcut', 2.5)
NBPT.setUnsetValues('potential', 'HardSphere')
BPT = PairTable(types=['P1'], parms=['k', 'r0', 'potential'])
BPT.setUnsetValues('k', 1.0)
BPT.setUnsetValues('r0', r0)
BPT.setUnsetValues('potential', potential)
system = System()
system.add_beads(x=x, y=y, z=z, types=t, bonds=bonds)
system.box = Box(cell_grid=(3, 3, 3))
system.box.lx = lx
system.box.ly = ly
system.box.lz = lz
system.BondedTable = BPT
system.NonBondedTable = NBPT
(x, y, z), (imx, imy, imz) = system.box.wrap_positions(x=x, y=y, z=z)
xarray = np.array(x, dtype=np.float)
yarray = np.array(y, dtype=np.float)
zarray = np.array(z, dtype=np.float)
system.box.neighbor_list.build_nlist(xarray, yarray, zarray, True)
PE = BondedPotentialEnergy(system)
U1 = sum(PE.compute(partial_indices=partial_indices))
self.assertAlmostEqual(U0, U1, delta=0.001)
def base_test(self, lx, ly, lz, N, dz, potential, r0):
dx = 1.0
dy = 0.5
x = np.array([i * dx for i in range(N)])
y = np.array([i * dy for i in range(N)])
z = np.array([dz * i - lz / 2.0 for i in range(N)])
t = [0] * N
bonds = [[i, j] for i, j in zip(range(N - 1), range(1, N))]
NBPT = PairTable(types=['P1'],
parms=['epsilon', 'rcut', 'sigma', 'potential'])
NBPT.setUnsetValues('epsilon', 1.0)
NBPT.setUnsetValues('sigma', 1.0)
NBPT.setUnsetValues('rcut', 2.5)
NBPT.setUnsetValues('potential', 'HardSphere')
BPT = PairTable(types=['P1'], parms=['k', 'r0', 'potential'])
BPT.setUnsetValues('k', 1.0)
BPT.setUnsetValues('r0', r0)
BPT.setUnsetValues('potential', potential)
system = System()
system.add_beads(x=x, y=y, z=z, types=t, bonds=bonds)
system.box = Box(cell_grid=(3, 3, 3))
system.box.lx = lx
system.box.ly = ly
system.box.lz = lz
system.BondedTable = BPT
system.NonBondedTable = NBPT
(x, y, z), (imx, imy, imz) = system.box.wrap_positions(x=x, y=y, z=z)
U0 = self.calc_all_potential(bonds, x, y, z, t, lx, ly, lz, BPT)
xarray = np.array(x, dtype=np.float)
yarray = np.array(y, dtype=np.float)
zarray = np.array(z, dtype=np.float)
system.box.neighbor_list.build_nlist(xarray, yarray, zarray, True)
PE = BondedPotentialEnergy(system)
U1 = sum(PE.compute())
return U0, U1
def test_trial_move(self):
lx = 8
ly = 11
lz = 9
dz = 1.1
r0 = 1.0
potential = 'Harmonic'
N = 10
ref_x = np.array([0.0] * N)
ref_y = np.array([0.0] * N)
ref_z = np.array([dz * i - lz / 2.0 for i in range(N)])
ref_t = [0] * N
ref_bonds = [[i, j] for i, j in zip(range(N - 1), range(1, N))]
N = 5
x = [0.0] * N
y = [0.0] * N
z = [dz * i - lz / 2.0 for i in range(N)]
t = [0] * N
bonds = [[i, j] for i, j in zip(range(N - 1), range(1, N))]
N_trial = 5
trial_x = [0.0] * N_trial
trial_y = [0.0] * N_trial
trial_z = [dz * 5 + dz * i - lz / 2.0 for i in range(N_trial)]
trial_t = [0] * N_trial
trial_bonds = [[i + N, j + N]
for i, j in zip(range(N_trial - 1), range(1, N_trial))]
trial_bonds += [[N, N + 1]]
NBPT = PairTable(types=['P1'],
parms=['epsilon', 'rcut', 'sigma', 'potential'])
NBPT.setUnsetValues('epsilon', 1.0)
NBPT.setUnsetValues('sigma', 1.0)
NBPT.setUnsetValues('rcut', 2.5)
NBPT.setUnsetValues('potential', 'HardSphere')
BPT = PairTable(types=['P1'], parms=['k', 'r0', 'potential'])
BPT.setUnsetValues('k', 1.0)
BPT.setUnsetValues('r0', r0)
BPT.setUnsetValues('potential', potential)
system = System()
system.add_beads(x=x, y=y, z=z, types=t, bonds=bonds)
system.box = Box(cell_grid=(3, 3, 3))
system.box.lx = lx
system.box.ly = ly
system.box.lz = lz
system.BondedTable = BPT
system.NonBondedTable = NBPT
system.trial_x = np.array([trial_x])
system.trial_y = np.array([trial_y])
system.trial_z = np.array([trial_z])
system.trial_types = np.array([trial_t])
system.trial_bond_pairlist = np.array(trial_bonds)
(ref_x, ref_y, ref_z), (imx, imy,
imz) = system.box.wrap_positions(x=ref_x,
y=ref_y,
z=ref_z)
U0 = self.calc_all_potential(ref_bonds, ref_x, ref_y, ref_z, ref_t, lx,
ly, lz, BPT)
PE = BondedPotentialEnergy(system)
U1 = sum(PE.compute())
U2 = sum(PE.compute(trial_move=True))
self.assertAlmostEqual(U0, U1 + U2, delta=0.001)