def get_part_caffeine_grimme_15A():
# Get a system and define scalings
system = get_system_caffeine()
nlist = NeighborList(system)
scalings = Scalings(system, 0.0, 1.0, 0.5)
# Initialize (random) parameters
r0_table = {
1: 1.001*angstrom,
6: 1.452*angstrom,
7: 1.397*angstrom,
8: 1.342*angstrom,
}
c6_table = {
1: 0.14*1e-3*kjmol*nanometer**6,
6: 1.75*1e-3*kjmol*nanometer**6,
7: 1.23*1e-3*kjmol*nanometer**6,
8: 0.70*1e-3*kjmol*nanometer**6,
}
r0s = np.zeros(24, float)
c6s = np.zeros(24, float)
for i in xrange(system.natom):
r0s[i] = r0_table[system.numbers[i]]
c6s[i] = c6_table[system.numbers[i]]
# Construct the pair potential and part
pair_pot = PairPotGrimme(r0s, c6s, 15*angstrom)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
# The pair function
def pair_fn(i, j, d):
r0 = (r0s[i]+r0s[j])
c6 = np.sqrt(c6s[i]*c6s[j])
return -1.1/(1.0 + np.exp(-20.0*(d/r0-1.0)))*c6/d**6
return system, nlist, scalings, part_pair, pair_fn
def get_part_caffeine_mm3_15A():
# Get a system and define scalings
system = get_system_caffeine()
nlist = NeighborList(system)
scalings = Scalings(system, 0.0, 1.0, 0.5)
# Initialize (random) parameters
rminhalf_table = {
1: 0.2245*angstrom,
6: 1.6000*angstrom,
7: 1.7000*angstrom,
8: 1.7682*angstrom
}
epsilon_table = {
1: -0.0460*kcalmol,
6: -0.2357*kcalmol,
7: -0.1970*kcalmol,
8: -0.1521*kcalmol,
}
sigmas = np.zeros(24, float)
epsilons = np.zeros(24, float)
onlypaulis = np.zeros(24, np.int32)
for i in xrange(system.natom):
sigmas[i] = rminhalf_table[system.numbers[i]]*(2.0)**(5.0/6.0)
epsilons[i] = epsilon_table[system.numbers[i]]
# Construct the pair potential and part
pair_pot = PairPotMM3(sigmas, epsilons, onlypaulis, 15*angstrom)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
# The pair function
def pair_fn(i, j, d):
sigma = sigmas[i]+sigmas[j]
epsilon = np.sqrt(epsilons[i]*epsilons[j])
x = (sigma/d)
return epsilon*(1.84e5*np.exp(-12.0/x)-2.25*x**6)
return system, nlist, scalings, part_pair, pair_fn
def get_part_caffeine_exprep_5A(amp_mix, amp_mix_coeff, b_mix, b_mix_coeff):
# Get a system and define scalings
system = get_system_caffeine()
nlist = NeighborList(system)
scalings = Scalings(system, 0.0, 1.0, 1.0)
# Initialize (random) parameters
amps = np.array([2.35, 410.0, 0.0, 421.0])
bs = np.array([4.46, 4.43, 0.0, 4.41])/angstrom
# Allocate some arrays for the pair potential
assert len(system.ffatypes) == 4
amp_cross = np.zeros((4, 4), float)
b_cross = np.zeros((4, 4), float)
# Construct the pair potential and part
pair_pot = PairPotExpRep(
system.ffatype_ids, amp_cross, b_cross, 5*angstrom, None,
amps, amp_mix, amp_mix_coeff, bs, b_mix, b_mix_coeff,
)
assert abs(np.diag(pair_pot.amp_cross) - amps).max() < 1e-10
assert abs(np.diag(pair_pot.b_cross) - bs).max() < 1e-10
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
# The pair function
def pair_fn(i0, i1, d):
amp0 = amps[system.ffatype_ids[i0]]
amp1 = amps[system.ffatype_ids[i1]]
b0 = bs[system.ffatype_ids[i0]]
b1 = bs[system.ffatype_ids[i1]]
if amp_mix == 0:
amp = np.sqrt(amp0*amp1)
elif amp0 == 0.0 or amp1 == 0.0:
amp = 0.0
elif amp_mix == 1:
cor = 1-amp_mix_coeff*abs(np.log(amp0/amp1))
amp = np.exp( (np.log(amp0)+np.log(amp1))/2*cor )
else:
raise NotImplementedError
if b_mix == 0:
b = (b0+b1)/2
elif amp0 == 0.0 or amp1 == 0.0:
b = 0.0
elif b_mix == 1:
cor = 1-b_mix_coeff*abs(np.log(amp0/amp1))
b = (b0+b1)/2*cor
else:
raise NotImplementedError
if amp == 0.0 or b == 0.0:
energy = 0.0
else:
energy = amp*np.exp(-b*d)
return energy
return system, nlist, scalings, part_pair, pair_fn
def get_part_caffeine_ei2_10A():
# Get a system and define scalings
system = get_system_caffeine()
nlist = NeighborList(system)
scalings = Scalings(system, 0.0, 1.0, 0.5)
dielectric = 1.0
# Initialize (random) parameters
system.charges = np.random.uniform(0, 1, system.natom)
system.charges -= system.charges.sum()
# Construct the pair potential and part
rcut = 10*angstrom
alpha = 0.0
pair_pot = PairPotEI(system.charges, alpha, rcut, dielectric=dielectric)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
# The pair function
def pair_fn(i, j, d):
return system.charges[i]*system.charges[j]*erfc(alpha*d)/d
return system, nlist, scalings, part_pair, pair_fn
def test_atselect_caffeine():
system = get_system_caffeine()
assert (system.get_indexes('C&=3%H')==np.array([11, 12, 13])).all()
assert (system.get_indexes('C&=2%N')==np.array([7, 9, 10])).all()
assert (system.get_indexes('O')==np.array([0, 1])).all()
assert (system.get_indexes('O&=1')==np.array([0, 1])).all()
assert (system.get_indexes('O&=1%C')==np.array([0, 1])).all()
assert (system.get_indexes('O&=1%(C&=3)')==np.array([0, 1])).all()
assert (system.get_indexes('O&=1%(C&=2%N)')==np.array([1])).all()
assert (system.get_indexes('O&=1%(C&=1%C)')==np.array([0])).all()
assert (system.get_indexes('C&=3')==np.array([6, 7, 8, 9, 10])).all()
assert (system.get_indexes('C&=1%C')==np.array([7, 8])).all()
assert (system.get_indexes('C&>1%C')==np.array([6])).all()
assert (system.get_indexes('C&<2%C')==np.array([7, 8, 9, 10, 11, 12, 13])).all()
assert (system.get_indexes('N&=2%C&=2')==np.array([5])).all()
assert (system.get_indexes('N&!=2')==np.array([2, 3, 4])).all()
assert (system.get_indexes('N|O')==np.array([0, 1, 2, 3, 4, 5])).all()
assert (system.get_indexes('N|8')==np.array([0, 1, 2, 3, 4, 5])).all()
assert (system.get_indexes('!0')==np.arange(system.natom)).all()
def test_atselect_caffeine():
system = get_system_caffeine()
assert (system.get_indexes('C&=3%H')==np.array([11, 12, 13])).all()
assert (system.get_indexes('C&=2%N')==np.array([7, 9, 10])).all()
assert (system.get_indexes('O')==np.array([0, 1])).all()
assert (system.get_indexes('O&=1')==np.array([0, 1])).all()
assert (system.get_indexes('O&=1%C')==np.array([0, 1])).all()
assert (system.get_indexes('O&=1%(C&=3)')==np.array([0, 1])).all()
assert (system.get_indexes('O&=1%(C&=2%N)')==np.array([1])).all()
assert (system.get_indexes('O&=1%(C&=1%C)')==np.array([0])).all()
assert (system.get_indexes('C&=3')==np.array([6, 7, 8, 9, 10])).all()
assert (system.get_indexes('C&=1%C')==np.array([7, 8])).all()
assert (system.get_indexes('C&>1%C')==np.array([6])).all()
assert (system.get_indexes('C&<2%C')==np.array([7, 8, 9, 10, 11, 12, 13])).all()
assert (system.get_indexes('N&=2%C&=2')==np.array([5])).all()
assert (system.get_indexes('N&!=2')==np.array([2, 3, 4])).all()
assert (system.get_indexes('N|O')==np.array([0, 1, 2, 3, 4, 5])).all()
assert (system.get_indexes('N|8')==np.array([0, 1, 2, 3, 4, 5])).all()
assert (system.get_indexes('!0')==np.arange(system.natom)).all()
def get_part_caffeine_ei3_10A():
# Get a system and define scalings
system = get_system_caffeine()
nlist = NeighborList(system)
scalings = Scalings(system, 0.0, 1.0, 0.5)
# Initialize (random) parameters
system.charges = np.random.uniform(0, 1, system.natom)
system.charges -= system.charges.sum()
#Set the atomic radii
radii = np.random.uniform(0,1,system.natom)
# Construct the pair potential and part
rcut = 10*angstrom
alpha = 0.0
pair_pot = PairPotEI(system.charges, alpha, rcut, radii=radii)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
# The pair function
def pair_fn(i, j, d):
r_ij = np.sqrt( pair_pot.radii[i]**2 + pair_pot.radii[j]**2 )
return system.charges[i]*system.charges[j]*erf(d/r_ij)/d
return system, nlist, scalings, part_pair, pair_fn
def get_part_caffeine_dampdisp_9A():
# Get a system and define scalings
system = get_system_caffeine()
nlist = NeighborList(system)
scalings = Scalings(system, 0.0, 1.0, 1.0)
# Initialize (very random) parameters
c6s = np.array([2.5, 27.0, 18.0, 13.0])
bs = np.array([2.5, 2.0, 0.0, 1.8])
vols = np.array([5, 3, 4, 5])*angstrom**3
# Allocate some arrays
assert system.nffatype == 4
c6_cross = np.zeros((4, 4), float)
b_cross = np.zeros((4, 4), float)
# Construct the pair potential and part
pair_pot = PairPotDampDisp(system.ffatype_ids, c6_cross, b_cross, 9*angstrom, None, c6s, bs, vols)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
# The pair function
def pair_fn(i0, i1, d):
c60 = c6s[system.ffatype_ids[i0]]
c61 = c6s[system.ffatype_ids[i1]]
b0 = bs[system.ffatype_ids[i0]]
b1 = bs[system.ffatype_ids[i1]]
vol0 = vols[system.ffatype_ids[i0]]
vol1 = vols[system.ffatype_ids[i1]]
ratio = vol0/vol1
c6 = 2*c60*c61/(c60/ratio+c61*ratio)
if b0 != 0 and b1 != 0:
b = 0.5*(b0+b1)
damp = 0
fac = 1
for k in xrange(7):
damp += (b*d)**k/fac
fac *= k+1
damp = 1 - np.exp(-b*d)*damp
return -c6/d**6*damp
else:
damp = 1
return -c6/d**6
return system, nlist, scalings, part_pair, pair_fn
def test_iter_paths3():
system = get_system_caffeine()
paths = set(iter_paths(system, 18, 19, 2))
assert all(len(path) == 3 for path in paths)
assert len(paths) == 1
assert paths == set([(18, 12, 19)])
def test_iter_paths2():
system = get_system_caffeine()
paths = set(iter_paths(system, 13, 5, 5))
assert all(len(path) == 6 for path in paths)
assert len(paths) == 2
assert paths == set([(13, 4, 8, 6, 7, 5), (13, 4, 9, 2, 7, 5)])
def test_iter_paths1():
system = get_system_caffeine()
paths = set(iter_paths(system, 2, 8, 3))
assert all(len(path) == 4 for path in paths)
assert len(paths) == 2
assert paths == set([(2, 7, 6, 8), (2, 9, 4, 8)])
def test_topology_caffeine():
system = get_system_caffeine()
check_topology_slow(system)
def test_iter_paths3():
system = get_system_caffeine()
paths = set(iter_paths(system, 18, 19, 2))
assert all(len(path) == 3 for path in paths)
assert len(paths) == 1
assert paths == set([(18, 12, 19)])
def test_iter_paths2():
system = get_system_caffeine()
paths = set(iter_paths(system, 13, 5, 5))
assert all(len(path) == 6 for path in paths)
assert len(paths) == 2
assert paths == set([(13, 4, 8, 6, 7, 5), (13, 4, 9, 2, 7, 5)])
def test_iter_paths1():
system = get_system_caffeine()
paths = set(iter_paths(system, 2, 8, 3))
assert all(len(path) == 4 for path in paths)
assert len(paths) == 2
assert paths == set([(2, 7, 6, 8), (2, 9, 4, 8)])
def test_topology_caffeine():
system = get_system_caffeine()
check_topology_slow(system)