def generate_basis_functions(ppdata):
class SimpleBasis(Basis):
def __init__(self, symbol, l_j):
Basis.__init__(self, symbol, 'simple', readxml=False)
self.generatordata = 'simple'
self.d = 0.02
self.ng = 160
rgd = self.get_grid_descriptor()
bf_j = self.bf_j
rcgauss = rgd.r_g[-1] / 3.0
gauss_g = np.exp(-(rgd.r_g / rcgauss)**2.0)
for l in l_j:
phit_g = rgd.r_g**l * gauss_g
norm = (rgd.integrate(phit_g**2) / (4 * np.pi))**0.5
phit_g /= norm
bf = BasisFunction(l, rgd.r_g[-1], phit_g, 'gaussian')
bf_j.append(bf)
#l_orb_j = [state.l for state in self.data['states']]
b1 = SimpleBasis(ppdata.symbol, ppdata.l_orb_j)
apaw = AtomPAW(ppdata.symbol, [ppdata.f_ln], h=0.05, rcut=9.0,
basis={ppdata.symbol: b1},
setups={ppdata.symbol : ppdata},
lmax=0, txt=None)
basis = apaw.extract_basis_functions()
return basis
def generate_basis_functions(ppdata):
class SimpleBasis(Basis):
def __init__(self, symbol, l_j):
Basis.__init__(self, symbol, 'simple', readxml=False)
self.generatordata = 'simple'
self.d = 0.02
self.ng = 160
rgd = self.get_grid_descriptor()
bf_j = self.bf_j
rcgauss = rgd.r_g[-1] / 3.0
gauss_g = np.exp(-(rgd.r_g / rcgauss)**2.0)
for l in l_j:
phit_g = rgd.r_g**l * gauss_g
norm = (rgd.integrate(phit_g**2) / (4 * np.pi))**0.5
phit_g /= norm
bf = BasisFunction(l, rgd.r_g[-1], phit_g, 'gaussian')
bf_j.append(bf)
#l_orb_j = [state.l for state in self.data['states']]
b1 = SimpleBasis(ppdata.symbol, ppdata.l_orb_j)
apaw = AtomPAW(ppdata.symbol, [ppdata.f_ln], h=0.05, rcut=9.0,
basis={ppdata.symbol: b1},
setups={ppdata.symbol: ppdata},
lmax=0, txt=None)
basis = apaw.extract_basis_functions()
return basis
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
def create_basis_functions(self):
class SimpleBasis(Basis):
def __init__(self, symbol, l_j):
Basis.__init__(self, symbol, 'simple', readxml=False)
self.generatordata = 'simple'
self.d = 0.02
self.ng = 160
rgd = self.get_grid_descriptor()
bf_j = self.bf_j
rcgauss = rgd.rcut / 3.0
gauss_g = np.exp(-(rgd.r_g / rcgauss)**2.0)
for l in l_j:
phit_g = rgd.r_g**l * gauss_g
norm = np.dot((rgd.r_g * phit_g)**2, rgd.dr_g)**.5
phit_g /= norm
bf = BasisFunction(l, rgd.rcut, phit_g, 'gaussian')
bf_j.append(bf)
b1 = SimpleBasis(self.symbol, range(max(self.l_j) + 1))
apaw = AtomPAW(self.symbol, [self.f_ln], h=0.05, rcut=9.0,
basis={self.symbol: b1},
setups={self.symbol : self},
lmax=0, txt=None)
basis = apaw.extract_basis_functions()
return basis
import numpy as np
x = np.linspace(0.0, 5.0, 1000)
dr = x[1] - x[0]
psi = pp.phit_j[0].map(x)
p = pp.pt_j[0].map(x)
from gpaw.atom.atompaw import AtomPAW
if 0:
f = 1.0 #1e-12
c = AtomPAW(
'H',
[[[2.0], [4.0]]],
#charge=1 - f,
h=0.04,
#setups='paw',
#setups='hgh',
setups={'H': s})
import pylab as pl
pl.plot(c.wfs.gd.r_g, c.hamiltonian.vt_sg[0])
pl.show()
raise SystemExit
#print 'test v201 Au.pz-d-hgh.UPF'
#s = UPFSetupData('Au.pz-d-hgh.UPF')
#print 'v201 ok'
#print 'test horrible version O.pz-mt.UPF'
#s = UPFSetupData('O.pz-mt.UPF')
# Load pseudopotential from Python module as string, then
# write the string to a file, then load the file.
def upf(upf_module, fname):
with open(fname, 'w') as fd:
fd.write(upf_module.ps_txt)
return UPFSetupData(fname)
if world.rank == 0: # This test is not really parallel
kwargs = dict(txt=None)
for setup in ['paw', 'hgh', upf(H_hgh, 'H.pz-hgh.UPF')]:
calc = AtomPAW('H', [[[1]]],
rcut=12.0,
h=0.05,
setups={'H': setup},
**kwargs)
tol = 5e-4 if setup in ['paw', 'hgh'
] else 1e-3 # horrible UPF right now
check('H %s' % setup, calc, [-0.233471], tol)
for setup in ['paw', 'hgh', upf(O_hgh, 'O.pz-hgh.UPF')]:
calc = AtomPAW('O', [[[2], [4]]],
rcut=10.0,
h=0.035,
setups={'O': setup},
**kwargs)
tol = 1e-3 if setup in ['paw', 'hgh'
] else 5e-3 # horrible UPF right now
check('O %s' % setup, calc, [-0.871362, -0.338381], tol)
def atompaw(setup, f_ln, rcut, **kwargs):
return AtomPAW(setup.symbol, [f_ln],
rcut=rcut,
setups={setup.symbol: setup},
**kwargs)
def upfplot(setup, show=True, calculate=False):
# A version of this, perhaps nicer, is in pseudopotential.py.
# Maybe it is not worth keeping this version
if isinstance(setup, dict):
setup = UPFSetupData(setup)
pp = setup.data
r0 = pp['r'].copy()
r0[0] = 1e-8
def rtrunc(array, rdividepower=0):
r = r0[:len(array)]
arr = divrl(array, rdividepower, r)
return r, arr
import pylab as pl
fig = pl.figure()
fig.canvas.set_window_title('%s - UPF setup for %s' %
(pp['fname'], setup.symbol))
vax = fig.add_subplot(221)
pax = fig.add_subplot(222)
rhoax = fig.add_subplot(223)
wfsax = fig.add_subplot(224)
r, v = rtrunc(pp['vlocal'])
vax.plot(r, v, label='vloc')
vscreened, rhocomp = screen_potential(r, v, setup.Nv)
icut = len(rhocomp)
vcomp = v.copy()
vcomp[:icut] -= vscreened
vax.axvline(r[icut], ls=':', color='k')
vax.plot(r, vcomp, label='vcomp')
vax.plot(r[:icut], vscreened, label='vscr')
vax.axis(xmin=0.0, xmax=6.0)
rhoax.plot(r[:icut], rhocomp[:icut], label='rhocomp')
for j, proj in enumerate(pp['projectors']):
r, p = rtrunc(proj.values, 0)
pax.plot(r, p, label='p%d [l=%d]' % (j + 1, proj.l))
for j, st in enumerate(pp['states']):
r, psi = rtrunc(st.values, 1)
wfsax.plot(r, r * psi, label='wf%d %s' % (j, st.label))
r, rho = rtrunc(pp['rhoatom'], 2)
wfsax.plot(r, r * rho, label='rho')
if calculate:
calc = AtomPAW(
setup.symbol,
[setup.f_ln],
# xc='PBE', # XXX does not support GGAs :( :( :(
setups={setup.symbol: setup},
h=0.08,
rcut=10.0)
r_g = calc.wfs.gd.r_g
basis = calc.extract_basis_functions()
wfsax.plot(r_g,
r_g * calc.density.nt_sg[0] * 4.0 * np.pi,
ls='--',
label='rho [calc]',
color='r')
splines = basis.tosplines()
for spline, bf in zip(splines, basis.bf_j):
wfsax.plot(r_g, r_g * spline.map(r_g), label=bf.type)
vax.legend(loc='best')
rhoax.legend(loc='best')
pax.legend(loc='best')
wfsax.legend(loc='best')
for ax in [vax, rhoax, pax, wfsax]:
ax.set_xlabel('r [Bohr]')
ax.axhline(0.0, ls=':', color='black')
vax.set_ylabel('potential')
pax.set_ylabel('projectors')
wfsax.set_ylabel(r'$r \psi(r), r n(r)$')
rhoax.set_ylabel('Comp charges')
fig.subplots_adjust(wspace=0.3)
if show:
pl.show()