def base_test(self,PT,lx,ly,lz,types=None,N=3,box_resize=None):
x,y,z,t = self.make_rubix(N=N,types=types)
U0 = self.calc_all_potential(x,y,z,t,lx,ly,lz,PT)
system = System()
system.add_beads(x=x,y=y,z=z,types=t)
system.box = Box(cell_grid=(3,3,3))
system.box.lx = lx
system.box.ly = ly
system.box.lz = lz
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)
system.NonBondedTable = PT
PE = NonBondedPotentialEnergy(system)
U1 = sum(PE.compute())
U2 = sum(PE.compute(ignore_neighbor_list=True))
if box_resize is None:
return U0,U1,U2
system.box.lx = box_resize[0]
system.box.ly = box_resize[1]
system.box.lz = box_resize[2]
U3 = self.calc_all_potential(x,y,z,t,system.box.lx,system.box.ly,system.box.lz,PT)
U4 = sum(PE.compute())
U5 = sum(PE.compute(ignore_neighbor_list=True))
return U0,U1,U2,U3,U4,U5
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 test_pbc_homog_HS_sigma155_partial(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
x,y,z,t = self.make_rubix(N=N,types=None)
U0 = 0
dist = self.calc_dist(3,4,x,y,z,lx,ly,lz)
U0+=self.hard_sphere(dist,eps,sig,rcut)
dist = self.calc_dist(4,5,x,y,z,lx,ly,lz)
U0+=self.hard_sphere(dist,eps,sig,rcut)
dist = self.calc_dist(3,5,x,y,z,lx,ly,lz)
U0+=self.hard_sphere(dist,eps,sig,rcut)
for bead_i in partial_indices:
for bead_j in range(len(x)):
if bead_j not in partial_indices:
dist = self.calc_dist(bead_i,bead_j,x,y,z,lx,ly,lz)
U0+=self.hard_sphere(dist,eps,sig,rcut)
system = System()
system.add_beads(x=x,y=y,z=z,types=t)
system.box = Box(cell_grid=(3,3,3))
system.box.lx = lx
system.box.ly = ly
system.box.lz = lz
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)
system.NonBondedTable = PT
PE = NonBondedPotentialEnergy(system)
U1 = sum(PE.compute(partial_indices=partial_indices))
self.assertAlmostEqual(U0,U1,delta=0.001)
def by_type_proximity(self, typeList):
''' Distribute a single molecule into multiple molecules based on proximity to a bead type
'''
if len(typeList) < 2:
raise ValueError('Need at least two types to distribute between!')
box = self.molecule.system.box
if box is None:
box = Box(L=1000)
x = self.molecule.x.compressed()
y = self.molecule.y.compressed()
z = self.molecule.z.compressed()
types = self.molecule.types.compressed()
indices = np.array(self.molecule.indices)
# index_groups will be passed to self.distribute_by_index. It must be initialized with the
# beads which are pre-grouped because they match a grouping type
index_groups = []
for i, typeVal in enumerate(typeList):
index_groups.append(list(indices[types == typeVal]))
# Need to combine all typeGroups. These beads are already grouped
# as they define the groups themselves
mask = (types == typeList[0])
for typeVal in typeList[1:]:
mask = np.logical_or(mask, types == typeVal)
# Beads to be grouped
x1Array = x[~mask]
y1Array = y[~mask]
z1Array = z[~mask]
indices1 = indices[~mask]
# Beads which are pre-grouped because they match a proximity type
x2Array = x[mask]
y2Array = y[mask]
z2Array = z[mask]
types2 = types[mask]
for i, (x1, y1, z1) in enumerate(zip(x1Array, y1Array, z1Array)):
idex, dist = n_closest(1, x1, y1, z1, x2Array, y2Array, z2Array,
box)
for j, typeVal in enumerate(typeList):
if types2[idex[0]] == typeVal:
index_groups[j].append(indices1[i])
break
return self.by_index(index_groups)
def test_pbc_hex_HS(self):
lx = 9
ly = 9
lz = 8
nz = 4
PT = PairTable(types=['P1','P2'],parms=['epsilon','rcut','sigma','potential'])
PT.setUnsetValues('epsilon',1.0)
PT.setUnsetValues('sigma',1.0)
PT.setUnsetValues('rcut',2.5)
PT.setUnsetValues('potential','HardSphere')
HS = HexagonalSurface()
molData, boxData = HS.build(lx,ly,nz,diameter=1.0,topType=0,bottomType=0,middleType=1)
x = molData['x']
y = molData['y']
z = molData['z']
t = molData['types']
lx = boxData['lx']
ly = boxData['ly']
U0 = self.calc_all_potential(x,y,z,t,lx,ly,lz,PT)
system = System()
system.add_beads(x=x,y=y,z=z,types=t)
system.box = Box(cell_grid=(3,3,3))
system.box.lx = lx
system.box.ly = ly
system.box.lz = lz
xarray = np.array(x,dtype=np.double)
yarray = np.array(y,dtype=np.double)
zarray = np.array(z,dtype=np.double)
system.box.neighbor_list.build_nlist(xarray,yarray,zarray,True)
system.NonBondedTable = PT
PE = NonBondedPotentialEnergy(system)
U1 = sum(PE.compute())
U2 = sum(PE.compute(ignore_neighbor_list=True))
self.assertAlmostEqual(U0,U2,delta=0.01)
self.assertAlmostEqual(U0,U1,delta=0.01)
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_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)