def get_potential(self, gd=None):
"""Create the Coulomb potential on the grid."""
if hasattr(self, 'potential'):
if gd == self.gd or gd is None:
# nothing changed
return self.potential
if gd is None:
gd = self.gd
assert gd.orthogonal
potential = gd.empty()
n = len(self)
pc_nc = np.empty((n, 3))
charge_n = np.empty((n))
for a, pc in enumerate(self):
pc_nc[a] = pc.position / Bohr
charge_n[a] = pc.charge
self.pc_nc = pc_nc
self.charge_n = charge_n
_gpaw.pc_potential(potential, pc_nc, charge_n, gd.beg_c, gd.end_c,
gd.h_cv.diagonal())
# save grid descriptor and potential for future use
self.potential = potential
self.gd = gd
return potential
def get_potential(self, gd=None):
"""Create the Coulomb potential on the grid."""
if hasattr(self, "potential"):
if gd == self.gd or gd is None:
# nothing changed
return self.potential
if gd is None:
gd = self.gd
assert gd.orthogonal
potential = gd.empty()
n = len(self)
pc_nc = np.empty((n, 3))
charge_n = np.empty((n))
for a, pc in enumerate(self):
pc_nc[a] = pc.position / Bohr
charge_n[a] = pc.charge
self.pc_nc = pc_nc
self.charge_n = charge_n
_gpaw.pc_potential(potential, pc_nc, charge_n, gd.beg_c, gd.end_c, gd.h_cv.diagonal())
# save grid descriptor and potential for future use
self.potential = potential
self.gd = gd
return potential
def calculate_potential(self, gd):
assert gd.orthogonal
self.vext_g = gd.zeros()
dcom_pv = self._molecule_distances(gd)
_gpaw.pc_potential(gd.beg_c,
gd.h_cv.diagonal().copy(), self.q_p, self.R_pv,
self.rc, self.rc2, self.width, self.vext_g, dcom_pv)
def get_forces(self, calc):
"""Calculate forces from QM charge density on point-charges."""
dens = calc.density
F_pv = np.zeros_like(self.R_pv)
gd = dens.finegd
_gpaw.pc_potential(gd.beg_c,
gd.h_cv.diagonal().copy(), self.q_p, self.R_pv,
self.rc, self.rc2, self.width, self.vext_g,
dens.rhot_g, F_pv)
gd.comm.sum(F_pv)
return F_pv * Hartree / Bohr
def pc_potential(self, beg_c, end_c, h_cv):
"""
Set the potential up on the grid. Distances in Bohr. Take the whole
list of charges, and compute all distances. User specific potential.
"""
# Create a grid having dim gd.end_c (finegd sent)
potential = np.zeros(end_c-beg_c)
pos = np.zeros(3)
h = np.array([h_cv[0,0], h_cv[1,1], h_cv[2,2]])
# Potential is setup via v_ales, defined in qmmm_potentials
_gpaw.pc_potential(potential,self.pc_nc,self.charge_n,beg_c,end_c,h)
return potential
def pc_potential(self, beg_c, end_c, h_cv):
""" Set the potential up on the grid. Create the empty potential
grid and pass on to the appropriate c code
"""
# All values in [Bohr]
potential = np.zeros(end_c - beg_c)
h = np.array([h_cv[0,0],h_cv[1,1],h_cv[2,2]])
C = self.atoms.cell.diagonal() / Bohr
# Only cubic cells work (ATM)
if self.qmmm_pbc == 2 or self.qmmm_pbc is None:
_gpaw.pc_potential(potential, self.pc_nc, self.charge_n, \
beg_c, end_c, h)
elif self.qmmm_pbc == 1:
_gpaw.wolf_potential(potential, self.pc_nc, self.charge_n, \
beg_c, end_c, h, C)
# Missing PBC input in WOLF schemes!
return potential
def calculate_potential(self, gd):
assert gd.orthogonal
self.vext_g = gd.zeros()
_gpaw.pc_potential(gd.beg_c,
gd.h_cv.diagonal().copy(), self.q_p, self.R_pv,
self.rc, self.rc2, self.width, self.vext_g)
def f(rc):
vext_G[:] = 0.0
_gpaw.pc_potential(beg_v, h_v, q_p, R_pv, rc, np.inf, 1.0, vext_G)
return -vext_G[0, 0, 0]
_gpaw.pc_potential(beg_v, h_v, q_p, R_pv, rc, np.inf, 1.0, vext_G)
return -vext_G[0, 0, 0]
d = (R_pv[0]**2).sum()**0.5
for rc in [0.9 * d, 1.1 * d]:
if d > rc:
v0 = q / d
else:
v0 = np.polyval(c[::-1], (d / rc)**2) * q / rc
equal(f(rc), v0, 1e-12)
F_pv = np.zeros((1, 3))
_gpaw.pc_potential(beg_v, h_v, q_p, R_pv, rc, np.inf, 1.0, vext_G, rhot_G,
F_pv)
eps = 0.0001
for v in range(3):
R_pv[0, v] += eps
ep = f(rc)
R_pv[0, v] -= 2 * eps
em = f(rc)
R_pv[0, v] += eps
F = -(ep - em) / (2 * eps) * h**3
equal(F, -F_pv[0, v], 1e-9)
# High-level test:
lih = Atoms('LiH')
lih[1].y += 1.64
lih.center(vacuum=3)
