def get_gamma(self, a=None):
"""
Return the gamma correlation matrix, i.e. phi(i) = gamma(i, j)*q(j)
"""
if a is not None:
self.update(a)
self.timer.start('get_gamma')
nat = len(self.a)
il, jl, dl, nl = get_neighbors(self.a, self.cutoff)
if il is None:
G = None
else:
G = np.zeros([nat, nat], dtype=float)
if self.cutoff is None:
for i, j, d in zip(il, jl, dl):
G[i, j] += 1.0/d
else:
for i, j, d in zip(il, jl, dl):
G[i, j] += 1.0*erfc(d/self.cutoff)/d
self.timer.stop('get_gamma')
return G
def get_gamma(self, a=None):
"""
Return the gamma correlation matrix, i.e. phi(i) = gamma(i, j)*q(j)
"""
if a is not None:
self.update(a)
self.timer.start('get_gamma')
nat = len(self.a)
il, jl, dl, nl = get_neighbors(self.a, self.cutoff)
if il is None:
G = None
else:
G = np.zeros([nat, nat], dtype=float)
if self.cutoff is None:
for i, j, d in zip(il, jl, dl):
G[i, j] += 1.0 / d
else:
for i, j, d in zip(il, jl, dl):
G[i, j] += 1.0 * erfc(d / self.cutoff) / d
self.timer.stop('get_gamma')
return G
def _update(self, a, q):
"""
Compute the electrostatic potential and field on each atom in a.
Parameters:
-----------
a: Hotbit Atoms object, or atoms object that implements the transform
and rotation interface.
q: Charges
"""
self.timer.start('direct_coulomb')
self.a = a
self.r_av = a.get_positions().copy()
self.q_a = q.copy()
nat = len(a)
il, jl, dl, nl = get_neighbors(a, self.cutoff)
if il is not None:
if self.cutoff is None:
phi = q[jl] / dl
dl **= 2
E = q[jl].reshape(-1, 1) * nl / dl.reshape(-1, 1)
else:
f = erfc(dl / self.cutoff)
df = 2 / sqrt(pi) * np.exp(-(dl /
self.cutoff)**2) / self.cutoff
phi = q[jl] * f / dl
E = q[jl] * (df + f / dl) / dl
E = E.reshape(-1, 1) * nl
self.phi_a = np.zeros(nat, dtype=float)
self.E_av = np.zeros([nat, 3], dtype=float)
if il is not None:
# FIXME!!! Is there some fast numpy magic to compute this?
for i in xrange(nat):
self.phi_a[i] = phi[il == i].sum()
self.E_av[i, :] = E[il == i].sum(axis=0)
self.timer.stop('direct_coulomb')
def _update(self, a, q):
"""
Compute the electrostatic potential and field on each atom in a.
Parameters:
-----------
a: Hotbit Atoms object, or atoms object that implements the transform
and rotation interface.
q: Charges
"""
self.timer.start('direct_coulomb')
self.a = a
self.r_av = a.get_positions().copy()
self.q_a = q.copy()
nat = len(a)
il, jl, dl, nl = get_neighbors(a, self.cutoff)
if il is not None:
if self.cutoff is None:
phi = q[jl]/dl
dl **= 2
E = q[jl].reshape(-1, 1)*nl/dl.reshape(-1, 1)
else:
f = erfc(dl/self.cutoff)
df = 2/sqrt(pi)*np.exp(-(dl/self.cutoff)**2)/self.cutoff
phi = q[jl]*f/dl
E = q[jl]*(df + f/dl)/dl
E = E.reshape(-1, 1)*nl
self.phi_a = np.zeros(nat, dtype=float)
self.E_av = np.zeros([nat, 3], dtype=float)
if il is not None:
# FIXME!!! Is there some fast numpy magic to compute this?
for i in xrange(nat):
self.phi_a[i] = phi[il == i].sum()
self.E_av[i, :] = E[il == i].sum(axis=0)
self.timer.stop('direct_coulomb')