import numpy as np
from ase import units
from ase.calculators.calculator import Calculator, all_changes
from ase.calculators.tip3p import TIP3P, angleHOH, rOH
__all__ = ['rOH', 'angleHOH', 'TIP4P', 'sigma0', 'epsilon0']
# Electrostatic constant and parameters:
k_c = units.Hartree * units.Bohr
qH = 0.52
A = 600e3 * units.kcal / units.mol
B = 610 * units.kcal / units.mol
sigma0 = (A / B)**(1 / 6.)
epsilon0 = B**2 / (4 * A)
# https://doi.org/10.1063/1.445869
[docs]class TIP4P(TIP3P):
def __init__(self, rc=7.0, width=1.0):
""" TIP4P potential for water.
:doi:`10.1063/1.445869`
Requires an atoms object of OHH,OHH, ... sequence
Correct TIP4P charges and LJ parameters set automatically.
Virtual interaction sites implemented in the following scheme:
Original atoms object has no virtual sites.
When energy/forces are requested:
* virtual sites added to temporary xatoms object
* energy / forces calculated
* forces redistributed from virtual sites to actual atoms object
This means you do not get into trouble when propagating your system
with MD while having to skip / account for massless virtual sites.
This also means that if using for QM/MM MD with GPAW, the EmbedTIP4P
class must be used.
"""
TIP3P.__init__(self, rc, width)
self.atoms_per_mol = 3
self.sites_per_mol = 4
self.energy = None
self.forces = None
def calculate(self, atoms=None,
properties=['energy', 'forces'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
assert (atoms.numbers[::3] == 8).all()
assert (atoms.numbers[1::3] == 1).all()
assert (atoms.numbers[2::3] == 1).all()
xpos = self.add_virtual_sites(atoms.positions)
xcharges = self.get_virtual_charges(atoms)
cell = atoms.cell
pbc = atoms.pbc
natoms = len(atoms)
nmol = natoms // 3
self.energy = 0.0
self.forces = np.zeros((4 * natoms // 3, 3))
C = cell.diagonal()
assert (cell == np.diag(C)).all(), 'not orthorhombic'
assert ((C >= 2 * self.rc) | ~pbc).all(), 'cutoff too large'
# Get dx,dy,dz from first atom of each mol to same atom of all other
# and find min. distance. Everything moves according to this analysis.
for a in range(nmol - 1):
D = xpos[(a + 1) * 4::4] - xpos[a * 4]
shift = np.zeros_like(D)
for i, periodic in enumerate(pbc):
if periodic:
shift[:, i] = np.rint(D[:, i] / C[i]) * C[i]
q_v = xcharges[(a + 1) * 4:]
# Min. img. position list as seen for molecule !a!
position_list = np.zeros(((nmol - 1 - a) * 4, 3))
for j in range(4):
position_list[j::4] += xpos[(a + 1) * 4 + j::4] - shift
# Make the smooth cutoff:
pbcRoo = position_list[::4] - xpos[a * 4]
pbcDoo = np.sum(np.abs(pbcRoo)**2, axis=-1)**(1 / 2)
x1 = pbcDoo > self.rc - self.width
x2 = pbcDoo < self.rc
x12 = np.logical_and(x1, x2)
y = (pbcDoo[x12] - self.rc + self.width) / self.width
t = np.zeros(len(pbcDoo))
t[x2] = 1.0
t[x12] -= y**2 * (3.0 - 2.0 * y)
dtdd = np.zeros(len(pbcDoo))
dtdd[x12] -= 6.0 / self.width * y * (1.0 - y)
self.energy_and_forces(a, xpos, position_list, q_v, nmol, t, dtdd)
if self.pcpot:
e, f = self.pcpot.calculate(xcharges, xpos)
self.energy += e
self.forces += f
f = self.redistribute_forces(self.forces)
self.results['energy'] = self.energy
self.results['forces'] = f
def energy_and_forces(self, a, xpos, position_list, q_v, nmol, t, dtdd):
""" energy and forces on molecule a from all other molecules.
cutoff is based on O-O Distance. """
# LJ part - only O-O interactions
epsil = np.tile([epsilon0], nmol - 1 - a)
sigma = np.tile([sigma0], nmol - 1 - a)
DOO = position_list[::4] - xpos[a * 4]
d2 = (DOO**2).sum(1)
d = np.sqrt(d2)
e_lj = 4 * epsil * (sigma**12 / d**12 - sigma**6 / d**6)
f_lj = (4 * epsil * (12 * sigma**12 / d**13 -
6 * sigma**6 / d**7) * t -
e_lj * dtdd)[:, np.newaxis] * DOO / d[:, np.newaxis]
self.forces[a * 4] -= f_lj.sum(0)
self.forces[(a + 1) * 4::4] += f_lj
# Electrostatics
e_elec = 0
all_cut = np.repeat(t, 4)
for i in range(4):
D = position_list - xpos[a * 4 + i]
d2_all = (D**2).sum(axis=1)
d_all = np.sqrt(d2_all)
e = k_c * q_v[i] * q_v / d_all
e_elec += np.dot(all_cut, e).sum()
e_f = e.reshape(nmol - a - 1, 4).sum(1)
F = (e / d_all * all_cut)[:, np.newaxis] * D / d_all[:, np.newaxis]
FOO = -(e_f * dtdd)[:, np.newaxis] * DOO / d[:, np.newaxis]
self.forces[(a + 1) * 4 + 0::4] += FOO
self.forces[a * 4] -= FOO.sum(0)
self.forces[(a + 1) * 4:] += F
self.forces[a * 4 + i] -= F.sum(0)
self.energy += np.dot(e_lj, t) + e_elec
def add_virtual_sites(self, pos):
# Order: OHHM,OHHM,...
# DOI: 10.1002/(SICI)1096-987X(199906)20:8
b = 0.15
xatomspos = np.zeros((4 * len(pos) // 3, 3))
for w in range(0, len(pos), 3):
r_i = pos[w] # O pos
r_j = pos[w + 1] # H1 pos
r_k = pos[w + 2] # H2 pos
n = (r_j + r_k) / 2 - r_i
n /= np.linalg.norm(n)
r_d = r_i + b * n
x = 4 * w // 3
xatomspos[x + 0] = r_i
xatomspos[x + 1] = r_j
xatomspos[x + 2] = r_k
xatomspos[x + 3] = r_d
return xatomspos
def get_virtual_charges(self, atoms):
charges = np.empty(len(atoms) * 4 // 3)
charges[0::4] = 0.00 # O
charges[1::4] = qH # H1
charges[2::4] = qH # H2
charges[3::4] = - 2 * qH # X1
return charges
def redistribute_forces(self, forces):
f = forces
b = 0.15
a = 0.5
pos = self.atoms.positions
for w in range(0, len(pos), 3):
r_i = pos[w] # O pos
r_j = pos[w + 1] # H1 pos
r_k = pos[w + 2] # H2 pos
r_ij = r_j - r_i
r_jk = r_k - r_j
r_d = r_i + b * (r_ij + a * r_jk) / np.linalg.norm(r_ij + a * r_jk)
r_id = r_d - r_i
gamma = b / np.linalg.norm(r_ij + a * r_jk)
x = w * 4 // 3
Fd = f[x + 3] # force on M
F1 = (np.dot(r_id, Fd) / np.dot(r_id, r_id)) * r_id
Fi = Fd - gamma * (Fd - F1) # Force from M on O
Fj = (1 - a) * gamma * (Fd - F1) # Force from M on H1
Fk = a * gamma * (Fd - F1) # Force from M on H2
f[x] += Fi
f[x + 1] += Fj
f[x + 2] += Fk
# remove virtual sites from force array
f = np.delete(f, list(range(3, f.shape[0], 4)), axis=0)
return f