# Grid is so small that domain decomposition cannot exceed 4 domains
assert world.size % 4 == 0
group, other = divmod(world.rank, 4)
ranks = np.arange(4*group, 4*(group+1))
domain_comm = world.new_communicator(ranks)
else:
domain_comm = world
gd = GridDescriptor((8, 1, 1), (8.0, 1.0, 1.0), comm=domain_comm)
a = gd.zeros()
dadx = gd.zeros()
a[:, 0, 0] = np.arange(gd.beg_c[0], gd.end_c[0])
gradx = Gradient(gd, v=0)
print a.itemsize, a.dtype, a.shape
print dadx.itemsize, dadx.dtype, dadx.shape
gradx.apply(a, dadx)
# a = [ 0. 1. 2. 3. 4. 5. 6. 7.]
#
# da
# -- = [-2.5 1. 1. 1. 1. 1. 1. -2.5]
# dx
dadx = gd.collect(dadx, broadcast=True)
assert dadx[3, 0, 0] == 1.0 and np.sum(dadx[:, 0, 0]) == 0.0
gd = GridDescriptor((1, 8, 1), (1.0, 8.0, 1.0), (1, 0, 1), comm=domain_comm)
dady = gd.zeros()
a = gd.zeros()
grady = Gradient(gd, v=1)
a[0, :, 0] = np.arange(gd.beg_c[1], gd.end_c[1]) - 1
class ADM12PoissonSolver(SolvationPoissonSolver):
"""Poisson solver with dielectric.
Following O. Andreussi, I. Dabo, and N. Marzari,
J. Chem. Phys. 136, 064102 (2012).
Warning: Not intended for production use, as it is not tested
thouroughly!
XXX TODO : * Correction for charged systems???
* Check: Can the polarization charge introduce a monopole?
* Convergence problems depending on eta. Apparently this
method works best with FFT as in the original Paper.
* Optimize numerics.
"""
def __init__(self,
nn=3,
relax='J',
eps=2e-10,
maxiter=1000,
remove_moment=None,
eta=.6,
use_charge_center=False):
"""Constructor for ADM12PoissonSolver.
Additional arguments not present in SolvationPoissonSolver:
eta -- linear mixing parameter
"""
adm12_warning = UserWarning(
'ADM12PoissonSolver is not tested thoroughly'
' and therefore not recommended for production code!')
warnings.warn(adm12_warning)
self.eta = eta
SolvationPoissonSolver.__init__(self,
nn,
relax,
eps,
maxiter,
remove_moment,
use_charge_center=use_charge_center)
def set_grid_descriptor(self, gd):
SolvationPoissonSolver.set_grid_descriptor(self, gd)
self.gradx = Gradient(gd, 0, 1.0, self.nn)
self.grady = Gradient(gd, 1, 1.0, self.nn)
self.gradz = Gradient(gd, 2, 1.0, self.nn)
def get_description(self):
if len(self.operators) == 0:
return 'uninitialized ADM12PoissonSolver'
else:
description = SolvationPoissonSolver.get_description(self)
return description.replace('solver with',
'ADM12 solver with dielectric and')
def _init(self):
if self._initialized:
return
self.rho_iter = self.gd.zeros()
self.d_phi = self.gd.empty()
return SolvationPoissonSolver._init(self)
def solve(self,
phi,
rho,
charge=None,
eps=None,
maxcharge=1e-6,
zero_initial_phi=False,
timer=None):
self._init()
if self.gd.pbc_c.all():
actual_charge = self.gd.integrate(rho)
if abs(actual_charge) > maxcharge:
raise NotImplementedError(
'charged periodic systems are not implemented')
return FDPoissonSolver.solve(self,
phi,
rho,
charge,
eps,
maxcharge,
zero_initial_phi,
timer=timer)
def solve_neutral(self, phi, rho, eps=2e-10, timer=None):
self._init()
self.rho = rho
return SolvationPoissonSolver.solve_neutral(self, phi, rho, eps)
def iterate2(self, step, level=0):
self._init()
if level == 0:
epsr, dx_epsr, dy_epsr, dz_epsr = self.dielectric.eps_gradeps
self.gradx.apply(self.phis[0], self.d_phi)
sp = dx_epsr * self.d_phi
self.grady.apply(self.phis[0], self.d_phi)
sp += dy_epsr * self.d_phi
self.gradz.apply(self.phis[0], self.d_phi)
sp += dz_epsr * self.d_phi
self.rho_iter = self.eta / (4. * np.pi) * sp + \
(1. - self.eta) * self.rho_iter
self.rhos[0][:] = (self.rho_iter + self.rho) / epsr
return SolvationPoissonSolver.iterate2(self, step, level)
# Grid is so small that domain decomposition cannot exceed 4 domains
assert world.size % 4 == 0
group, other = divmod(world.rank, 4)
ranks = np.arange(4 * group, 4 * (group + 1))
domain_comm = world.new_communicator(ranks)
else:
domain_comm = world
gd = GridDescriptor((8, 1, 1), (8.0, 1.0, 1.0), comm=domain_comm)
a = gd.zeros()
dadx = gd.zeros()
a[:, 0, 0] = np.arange(gd.beg_c[0], gd.end_c[0])
gradx = Gradient(gd, v=0)
print a.itemsize, a.dtype, a.shape
print dadx.itemsize, dadx.dtype, dadx.shape
gradx.apply(a, dadx)
# a = [ 0. 1. 2. 3. 4. 5. 6. 7.]
#
# da
# -- = [-2.5 1. 1. 1. 1. 1. 1. -2.5]
# dx
dadx = gd.collect(dadx, broadcast=True)
assert dadx[3, 0, 0] == 1.0 and np.sum(dadx[:, 0, 0]) == 0.0
gd = GridDescriptor((1, 8, 1), (1.0, 8.0, 1.0), (1, 0, 1), comm=domain_comm)
dady = gd.zeros()
a = gd.zeros()
grady = Gradient(gd, v=1)
a[0, :, 0] = np.arange(gd.beg_c[1], gd.end_c[1]) - 1