def _generate(symbol, xc, configuration, projectors, radii,
scalar_relativistic, alpha, r0, nderiv0, pseudize, rcore,
core_hole, output):
if isinstance(output, str):
output = open(output, 'w')
aea = AllElectronAtom(symbol, xc, configuration=configuration, log=output)
gen = PAWSetupGenerator(aea,
projectors,
scalar_relativistic,
core_hole,
fd=output)
gen.construct_shape_function(alpha, radii, eps=1e-10)
gen.calculate_core_density()
gen.find_local_potential(r0, nderiv0)
gen.add_waves(radii)
gen.pseudize(pseudize[0], pseudize[1], rcore=rcore)
gen.construct_projectors(rcore)
return gen
def ip(symbol, fd, setup):
xc = 'LDA'
aea = AllElectronAtom(symbol, log=fd)
aea.initialize()
aea.run()
aea.refine()
aea.scalar_relativistic = True
aea.refine()
energy = aea.ekin + aea.eH + aea.eZ + aea.exc
eigs = []
for l, channel in enumerate(aea.channels):
n = l + 1
for e, f in zip(channel.e_n, channel.f_n):
if f == 0:
break
eigs.append((e, n, l))
n += 1
e0, n0, l0 = max(eigs)
aea = AllElectronAtom(symbol, log=fd)
aea.add(n0, l0, -1)
aea.initialize()
aea.run()
aea.refine()
aea.scalar_relativistic = True
aea.refine()
IP = aea.ekin + aea.eH + aea.eZ + aea.exc - energy
IP *= Ha
s = create_setup(symbol, type=setup, xc=xc)
f_ln = defaultdict(list)
for l, f in zip(s.l_j, s.f_j):
if f:
f_ln[l].append(f)
f_sln = [[f_ln[l] for l in range(1 + max(f_ln))]]
calc = AtomPAW(symbol, f_sln, xc=xc, txt=fd, setups=setup)
energy = calc.results['energy']
# eps_n = calc.wfs.kpt_u[0].eps_n
f_sln[0][l0][-1] -= 1
calc = AtomPAW(symbol, f_sln, xc=xc, charge=1, txt=fd, setups=setup)
IP2 = calc.results['energy'] - energy
return IP, IP2
from gpaw.atom.aeatom import AllElectronAtom, c
from gpaw.test import equal
Z = 79 # gold atom
kwargs = dict(alpha2=150 * Z**2, ngauss=100)
# Test Schroedinger equation:
aea = AllElectronAtom(Z, log=None)
aea.initialize(**kwargs)
errors = []
for channel in aea.channels:
channel.solve(-Z)
for n in range(7):
e = channel.e_n[n]
e0 = -0.5 * Z**2 / (n + channel.l + 1)**2
errors.append(abs(e / e0 - 1))
equal(max(errors), 0, 2.0e-5)
# Test Dirac equation:
aea = AllElectronAtom(Z, dirac=True, log=None)
aea.initialize(**kwargs)
errors = []
for channel in aea.channels:
channel.solve(-Z)
for n in range(7):
e = channel.e_n[n]
if channel.k > 0:
n += 1
e0 = (1 +
from __future__ import print_function
from gpaw.atom.aeatom import AllElectronAtom, c
from gpaw.test import equal
Z = 79 # gold atom
kwargs = dict(ngpts=5000, alpha2=1000 * Z**2, ngauss=200)
# Test Schroedinger equation:
aea = AllElectronAtom(Z, log=None)
aea.initialize(**kwargs)
errors = []
for channel in aea.channels:
channel.solve(-Z)
for n in range(7):
e = channel.e_n[n]
e0 = -0.5 * Z**2 / (n + channel.l + 1)**2
errors.append(abs(e / e0 - 1))
print(max(errors))
equal(max(errors), 0, 2.0e-5)
# Test Dirac equation:
aea = AllElectronAtom(Z, dirac=True, log=None)
aea.initialize(**kwargs)
errors = []
for channel in aea.channels:
channel.solve(-Z)
for n in range(7):
e = channel.e_n[n]
if channel.k > 0:
symbol = args[0]
kwargs = {'xc': opt.xc_functional}
aea = AEA(symbol, **kwargs)
aea.run()
gen = Generator(aea)
gen.generate()
if opt.plot:
gen.plot()
if __name__ == '__main__':
#main()
aea = AllElectronAtom('H')
#aea.add(2, 1, 0)
#aea.initialize()
aea.run()
#g = PAWSetupGenerator(aea, [(1, 0, 0.8)], 1)
g = PAWSetupGenerator(aea, [], 0, 0.8)
g.generate()
#g.plot()
setup = g.make_paw_setup()
from ase.data.molecules import molecule
from gpaw import GPAW
a = molecule('H', pbc=1, magmoms=[0])
a.center(vacuum=2)
a.set_calculator(
GPAW(setups={0: setup}))
# creates: paw_note.pdf
import subprocess
import matplotlib.pyplot as plt
from gpaw.atom.aeatom import AllElectronAtom
ae = AllElectronAtom('Pt')
ae.run()
ae.plot_wave_functions(show=False)
rcut = 2.5
lim = [0, 3.5, -2, 4]
plt.plot([rcut, rcut], lim[2:], 'k--', label='_nolegend_')
plt.axis(lim)
plt.text(0.6, 2, '[Pt] = [Xe]4f$^{14}$5d$^9$6s$^1$')
plt.savefig('Pt.png', dpi=80)
try:
subprocess.run(
'pdflatex -interaction=nonstopmode paw_note > /dev/null && '
'bibtex paw_note > /dev/null && '
'pdflatex -interaction=nonstopmode paw_note > /dev/null && '
'pdflatex -interaction=nonstopmode paw_note > /dev/null && '
'cp paw_note.pdf ..',
shell=True,
check=True)
except subprocess.CalledProcessError:
subprocess.run('echo "No pdflatex" > paw_note.pdf; cp paw_note.pdf ..',
shell=True)