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)
plt.xlabel(r'h [\AA]')
plt.ylabel('energy [eV]')
plt.legend(loc='best')
plt.subplot(312)
plt.semilogy(h, np.abs(data['Fegg']).max(axis=1), '-o',
label=r'$|\mathbf{F}_{egg}|$')
plt.semilogy(h, np.abs(data['Fdimer'].sum(axis=2)).max(axis=1), '-o',
label=r'$|\mathbf{F}_1 + \mathbf{F}_2|$')
#plt.title('Forces')
plt.xlabel(r'h [\AA]')
plt.ylabel(r'force [eV/\AA]')
plt.legend(loc='best')
plt.subplot(313)
d = ddimer0[-1]
plt.plot(h, ddimer0, '-o')
#plt.title('Bond length')
plt.xlabel(r'h [\AA]')
plt.axis(ymin=d * 0.98, ymax=d * 1.02)
plt.ylabel(r'bond length [\AA]')
plt.savefig('../_static/setups-data/%s-dimer-eggbox.png' % symbol, dpi=dpi)
#plt.show()
args = sys.argv[1:]
if len(args) == 0:
args = parameters.keys()
for symbol in args:
make_page(symbol)
fit = (5, 0.02)
w = 0.06
ecut = 1200
kd = 8.0
tag = 'dcdft_%s_gpaw_pw' % xc.lower()
task = Task(
calcfactory=Factory(xc=xc,
mode=PW(ecut),
occupations=FermiDirac(w),
maxiter=250,
kptdensity=kd,
),
tag=tag,
fit=fit,
use_lock_files=True,
)
if __name__ == '__main__':
if element is None:
keys = set(parameters.keys()).intersection(set(task.collection.names))
for s in elements_slow:
keys.remove(s) # those are slow, run separately
else:
keys = [element]
task.run(keys)
# plt.title('Energy differences')
plt.xlabel(u"h [Å]")
plt.ylabel("energy [eV]")
plt.legend(loc="best")
plt.subplot(312)
plt.semilogy(h, np.abs(data["Fegg"]).max(axis=1), "-o", label=r"$|\mathbf{F}_{egg}|$")
plt.semilogy(h, np.abs(data["Fdimer"].sum(axis=2)).max(axis=1), "-o", label=r"$|\mathbf{F}_1 + \mathbf{F}_2|$")
# plt.title('Forces')
plt.xlabel(u"h [Å]")
plt.ylabel(u"force [eV/Å]")
plt.legend(loc="best")
plt.subplot(313)
d = ddimer0[-1]
plt.plot(h, ddimer0, "-o")
# plt.title('Bond length')
plt.xlabel(u"h [Å]")
plt.axis(ymin=d * 0.98, ymax=d * 1.02)
plt.ylabel(u"bond length [Å]")
plt.savefig("../_static/setups-data/%s-dimer-eggbox.png" % symbol, dpi=dpi)
# plt.show()
args = sys.argv[1:]
if len(args) == 0:
args = parameters.keys()
for symbol in args:
make_page(symbol)
fit = (5, 0.02)
w = 0.06
ecut = 1200
kd = 8.0
tag = 'dcdft_%s_gpaw_pw' % xc.lower()
task = Task(
calcfactory=Factory(
xc=xc,
mode=PW(ecut),
occupations=FermiDirac(w),
maxiter=250,
kptdensity=kd,
),
tag=tag,
fit=fit,
use_lock_files=True,
)
if __name__ == '__main__':
if element is None:
keys = set(parameters.keys()).intersection(set(task.collection.names))
for s in elements_slow:
keys.remove(s) # those are slow, run separately
else:
keys = [element]
task.run(keys)
def main():
parser = OptionParser(usage='%prog [OPTION...] [SYMBOL...]',
description=description)
parser.add_option('--xc',
metavar='FUNCTIONAL',
default='PBE',
help='generate basis sets for FUNCTIONAL[=%default]')
parser.add_option('--from',
metavar='SYMBOL',
dest='_from',
help='generate starting from SYMBOL if generating '
'for all elements')
opts, symbols = parser.parse_args()
if len(symbols) == 0:
symbols = sorted(parameters.keys())
othersymbols = []
for symbol in parameters_extra:
name = parameters_extra[symbol]['name']
code = '%s.%s' % (symbol, name)
othersymbols.append(code)
trouble = set(['Os.8', 'Ta.5', 'V.5', 'W.6', 'Ir.9'])
othersymbols = [
symbol for symbol in othersymbols if symbol not in trouble
]
symbols.extend(sorted(othersymbols))
if opts._from:
index = symbols.index(opts._from)
symbols = symbols[index:]
specifications = []
for sym in symbols:
try:
s = SetupData(sym, opts.xc)
except RuntimeError as e:
if str(e).startswith('Could not find'):
#print 'No %s' % sym
continue
else:
raise
# One could include basis functions also for the ``virtual'' states
# (marked with negative n)
jvalues = []
jextra = []
for j in range(len(s.f_j)):
if s.eps_j[j] < 0:
jvalues.append(j)
if s.f_j[j] == 0.0 and s.n_j[j] > 0:
jextra.append(j)
if len(jextra) > 0:
specifications.append(BasisSpecification(s, jvalues, jextra))
#print sym, jvalues
# XXX check whether automatic settings coincide with those of official
# setups distribution
#bm = BasisMaker(sym, ''
if world.rank == 0:
print('Generating basis sets for: %s' %
' '.join(spec.setup.symbol for spec in specifications))
sys.stdout.flush()
world.barrier()
for i, spec in enumerate(specifications):
if i % world.size != world.rank:
continue
if world.size > 1:
print(world.rank, spec)
else:
print(spec)
gtxt = None
# XXX figure out how to accept Ag.11
tokens = spec.setup.symbol.split('.')
sym = tokens[0]
if len(tokens) == 1:
p = parameters
name = 'pvalence'
elif len(tokens) == 2:
p = parameters_extra
name = '%s.pvalence' % tokens[1]
else:
raise ValueError('Strange setup specification')
type = 'dz' # XXXXXXXXX
bm = BasisMaker(sym,
'%s.%s' % (name, type),
run=False,
gtxt=gtxt,
xc=opts.xc)
bm.generator.run(write_xml=False, use_restart_file=False, **p[sym])
basis = bm.generate(2, 0, txt=None, jvalues=spec.jvalues)
basis.write_xml()
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)