def test_pbc_homog_HS_sigma155_trial_move(self):
lx = 10
ly = 11
lz = 10
partial_indices = [3,4,5]
eps = 1.0
sig = 1.55
rcut = 2.5
PT = PairTable(types=['P1'],parms=['epsilon','rcut','sigma','potential'])
PT.setUnsetValues('epsilon',eps)
PT.setUnsetValues('sigma',sig)
PT.setUnsetValues('rcut',rcut)
PT.setUnsetValues('potential','HardSphere')
N = 3
ref_x,ref_y,ref_z,ref_t = self.make_rubix(N=N,types=None)
x1 = list(ref_x)
y1 = list(ref_y)
z1 = list(ref_z)
t1 = list(ref_t)
x2 = []; y2 = []; z2 = []; t2 = [];
trial_indices = [3,3,8] #equivalent to 3,4,10
for idex in trial_indices:
x2.append(x1.pop(idex))
y2.append(y1.pop(idex))
z2.append(z1.pop(idex))
t2.append(t1.pop(idex))
U0 = 0
dist = self.calc_dist(3,4,ref_x,ref_y,ref_z,lx,ly,lz)
U0+=self.hard_sphere(dist,eps,sig,rcut)
dist = self.calc_dist(4,10,ref_x,ref_y,ref_z,lx,ly,lz)
U0+=self.hard_sphere(dist,eps,sig,rcut)
dist = self.calc_dist(3,10,ref_x,ref_y,ref_z,lx,ly,lz)
U0+=self.hard_sphere(dist,eps,sig,rcut)
for bead_i in range(len(x2)):
for bead_j in range(len(x1)):
dx = abs(x2[bead_i] - x1[bead_j])
dy = abs(y2[bead_i] - y1[bead_j])
dz = abs(z2[bead_i] - z1[bead_j])
if dx>lx/2.0:
dx-=lx
if dy>ly/2.0:
dy-=ly
if dz>lz/2.0:
dz-=lz
dist = sqrt(dx*dx+dy*dy+dz*dz)
U0+=self.hard_sphere(dist,eps,sig,rcut)
system = System()
system.add_beads(x=x1,y=y1,z=z1,types=t1)
system.box = Box(cell_grid=(3,3,3))
system.box.lx = lx
system.box.ly = ly
system.box.lz = lz
system.trial_x = np.array([x2],dtype=np.float)
system.trial_y = np.array([y2],dtype=np.float)
system.trial_z = np.array([z2],dtype=np.float)
system.trial_types = np.array([t2])
system.trial_bonds = []
xarray = np.array(x1,dtype=np.float)
yarray = np.array(y1,dtype=np.float)
zarray = np.array(z1,dtype=np.float)
system.box.neighbor_list.build_nlist(xarray,yarray,zarray,True)
system.NonBondedTable = PT
PE = NonBondedPotentialEnergy(system)
U1 = sum(PE.compute(trial_move=True))
self.assertAlmostEqual(U0,U1,delta=0.001)
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)