def generate_setup(self):
if mpi.rank == 0:
gen = Generator(self.symbol, 'PBE', scalarrel=True)
gen.run(logderiv=True, **parameters[self.symbol])
data = analyse(gen, show=False)
g = np.arange(gen.N)
r_g = gen.r
dr_g = gen.beta * gen.N / (gen.N - g)**2
rcutcomp = gen.rcutcomp
rcutfilter = gen.rcutfilter
# Find cutoff for core density:
if gen.Nc == 0:
rcore = 0.5
else:
N = 0.0
g = gen.N - 1
while N < 1e-7:
N += np.sqrt(4 * np.pi) * gen.nc[g] * r_g[g]**2 * dr_g[g]
g -= 1
rcore = r_g[g]
nlfer = []
for j in range(gen.njcore):
nlfer.append((gen.n_j[j], gen.l_j[j], gen.f_j[j], gen.e_j[j],
0.0))
for n, l, f, eps in zip(gen.vn_j, gen.vl_j, gen.vf_j, gen.ve_j):
nlfer.append((n, l, f, eps, gen.rcut_l[l]))
self.data = dict(Z=gen.Z,
Nv=gen.Nv,
Nc=gen.Nc,
rcutcomp=rcutcomp,
rcutfilter=rcutfilter,
rcore=rcore,
Ekin=gen.Ekin,
Epot=gen.Epot,
Exc=gen.Exc,
nlfer=nlfer)
def generate_setup(self):
if mpi.rank == 0:
gen = Generator(self.symbol, 'PBE', scalarrel=True)
gen.run(logderiv=True, **parameters[self.symbol])
data = analyse(gen, show=False)
g = np.arange(gen.N)
r_g = gen.r
dr_g = gen.beta * gen.N / (gen.N - g)**2
rcutcomp = gen.rcutcomp
rcutfilter = gen.rcutfilter
# Find cutoff for core density:
if gen.Nc == 0:
rcore = 0.5
else:
N = 0.0
g = gen.N - 1
while N < 1e-7:
N += np.sqrt(4 * np.pi) * gen.nc[g] * r_g[g]**2 * dr_g[g]
g -= 1
rcore = r_g[g]
nlfer = []
for j in range(gen.njcore):
nlfer.append(
(gen.n_j[j], gen.l_j[j], gen.f_j[j], gen.e_j[j], 0.0))
for n, l, f, eps in zip(gen.vn_j, gen.vl_j, gen.vf_j, gen.ve_j):
nlfer.append((n, l, f, eps, gen.rcut_l[l]))
self.data = dict(Z=gen.Z,
Nv=gen.Nv,
Nc=gen.Nc,
rcutcomp=rcutcomp,
rcutfilter=rcutfilter,
rcore=rcore,
Ekin=gen.Ekin,
Epot=gen.Epot,
Exc=gen.Exc,
nlfer=nlfer)
def main():
parser = build_parser()
opt, args = parser.parse_args()
import sys
from gpaw.atom.generator import Generator
from gpaw.atom.configurations import parameters, tf_parameters
from gpaw.atom.all_electron import AllElectron
from gpaw import ConvergenceError
if args:
atoms = args
else:
atoms = parameters.keys()
bad_density_warning = """\
Problem with initial electron density guess! Try to run the program
with the '-nw' option (non-scalar-relativistic calculation + write
density) and then try again without the '-n' option (this will
generate a good initial guess for the density)."""
for symbol in atoms:
scalarrel = not opt.non_scalar_relativistic
corehole = None
if opt.core_hole is not None:
state, occ = opt.core_hole.split(',')
# Translate corestate string ('1s') to n and l:
ncorehole = int(state[0])
lcorehole = 'spdf'.find(state[1])
fcorehole = float(occ)
corehole = (ncorehole, lcorehole, fcorehole)
if opt.all_electron_only:
a = AllElectron(symbol, opt.xcfunctional, scalarrel, corehole,
opt.configuration, not opt.write_files, '-',
opt.points_per_node,
opt.orbital_free, opt.tw_coefficient)
try:
a.run()
except ConvergenceError:
print(bad_density_warning, file=sys.stderr)
continue
g = Generator(symbol, opt.xcfunctional, scalarrel, corehole,
opt.configuration, not opt.write_files, '-',
opt.points_per_node, orbital_free=opt.orbital_free,
tw_coeff=opt.tw_coefficient)
if opt.orbital_free:
p = tf_parameters.get(symbol, {'rcut': 0.9})
else:
p = parameters.get(symbol, {})
if opt.core is not None:
p['core'] = opt.core
if opt.radius is not None:
p['rcut'] = [float(x) for x in opt.radius.split(',')]
if opt.extra_projectors is not None:
extra = {}
if opt.extra_projectors != '':
for l, x in enumerate(opt.extra_projectors.split(';')):
if x != '':
extra[l] = [float(y) for y in x.split(',')]
p['extra'] = extra
if opt.normconserving is not None:
p['normconserving'] = opt.normconserving
if opt.filter is not None:
p['filter'] = [float(x) for x in opt.filter.split(',')]
if opt.compensation_charge_radius is not None:
p['rcutcomp'] = opt.compensation_charge_radius
if opt.zero_potential is not None:
vbar = opt.zero_potential.split(',')
p['vbar'] = (vbar[0], float(vbar[1]))
if opt.empty_states is not None:
p['empty_states'] = opt.empty_states
try:
g.run(logderiv=opt.logarithmic_derivatives,
exx=opt.exact_exchange, name=opt.name,
use_restart_file=opt.use_restart_file,
**p)
except ConvergenceError:
print(bad_density_warning, file=sys.stderr)
except RuntimeError as m:
if len(m.__str__()) == 0:
raise
print(m)
if opt.plot:
from gpaw.atom.analyse_setup import analyse
analyse(g, show=True)
def main():
parser = build_parser()
opt, args = parser.parse_args()
import sys
from gpaw.atom.generator import Generator
from gpaw.atom.configurations import parameters, tf_parameters
from gpaw.atom.all_electron import AllElectron
from gpaw import ConvergenceError
if args:
atoms = args
else:
atoms = parameters.keys()
bad_density_warning = """\
Problem with initial electron density guess! Try to run the program
with the '-nw' option (non-scalar-relativistic calculation + write
density) and then try again without the '-n' option (this will
generate a good initial guess for the density)."""
for symbol in atoms:
scalarrel = not opt.non_scalar_relativistic
corehole = None
if opt.core_hole is not None:
state, occ = opt.core_hole.split(',')
# Translate corestate string ('1s') to n and l:
ncorehole = int(state[0])
lcorehole = 'spdf'.find(state[1])
fcorehole = float(occ)
corehole = (ncorehole, lcorehole, fcorehole)
if opt.all_electron_only:
a = AllElectron(symbol, opt.xcfunctional, scalarrel, corehole,
opt.configuration, not opt.write_files, '-',
opt.points_per_node,
opt.orbital_free, opt.tf_coefficient)
try:
a.run()
except ConvergenceError:
print(bad_density_warning, file=sys.stderr)
continue
g = Generator(symbol, opt.xcfunctional, scalarrel, corehole,
opt.configuration, not opt.write_files, '-',
opt.points_per_node, orbital_free=opt.orbital_free,
tf_coeff=opt.tf_coefficient)
if opt.orbital_free:
p = tf_parameters.get(symbol, {'rcut': 0.9})
else:
p = parameters.get(symbol, {})
if opt.core is not None:
p['core'] = opt.core
if opt.radius is not None:
p['rcut'] = [float(x) for x in opt.radius.split(',')]
if opt.extra_projectors is not None:
extra = {}
if opt.extra_projectors != '':
for l, x in enumerate(opt.extra_projectors.split(';')):
if x != '':
extra[l] = [float(y) for y in x.split(',')]
p['extra'] = extra
if opt.normconserving is not None:
p['normconserving'] = opt.normconserving
if opt.filter is not None:
p['filter'] = [float(x) for x in opt.filter.split(',')]
if opt.compensation_charge_radius is not None:
p['rcutcomp'] = opt.compensation_charge_radius
if opt.zero_potential is not None:
vbar = opt.zero_potential.split(',')
p['vbar'] = (vbar[0], float(vbar[1]))
if opt.empty_states is not None:
p['empty_states'] = opt.empty_states
try:
g.run(logderiv=opt.logarithmic_derivatives,
exx=opt.exact_exchange, name=opt.name,
use_restart_file=opt.use_restart_file,
**p)
except ConvergenceError:
print(bad_density_warning, file=sys.stderr)
except RuntimeError, m:
if len(m.__str__()) == 0:
raise
print(m)
if opt.plot:
from gpaw.atom.analyse_setup import analyse
analyse(g, show=True)
