def upfplot(setup, show=True):
# 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()
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, psi, label='wf%d %s' % (j, st.label))
r, rho = rtrunc(pp['rhoatom'], 2)
wfsax.plot(r, rho, label='rho')
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('WF / density')
rhoax.set_ylabel('Comp charges')
#fig.canvas.set_window_title(fname) remember fname in setup
fig.subplots_adjust(wspace=0.3)
if show:
pl.show()
def __init__(self, data):
# data can be string (filename)
# or dict (that's what we are looking for).
# Maybe just a symbol would also be fine if we know the
# filename to look for.
if isinstance(data, basestring):
data = parse_upf(data)
assert isinstance(data, dict)
self.data = data # more or less "raw" data from the file
self.name = 'upf'
header = data['header']
keys = header.keys()
keys.sort()
self.symbol = header['element']
self.Z = atomic_numbers[self.symbol]
self.Nv = header['z_valence']
self.Nc = self.Z - self.Nv
self.Delta0 = -self.Nv / np.sqrt(4.0 * np.pi) # like hgh
self.rcut_j = [data['r'][len(proj.values) -1]
for proj in data['projectors']]
beta = 0.1 # XXX nice parameters?
N = 4 * 450 # XXX
# This is "stolen" from hgh. Figure out something reasonable
#rgd = AERadialGridDescriptor(beta / N, 1.0 / N, N,
# default_spline_points=100)
from gpaw.atom.radialgd import EquidistantRadialGridDescriptor
rgd = EquidistantRadialGridDescriptor(0.02)
self.rgd = rgd
# Whyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy???
# What abominable part of the code requires the states
# to be ordered like this?
self.jargs = self.get_jargs()
projectors = [data['projectors'][jarg] for jarg in self.jargs]
if projectors:
self.l_j = [proj.l for proj in projectors]
self.pt_jg = []
for proj in projectors:
val = proj.values.copy()
val /= 2.
val[1:] /= data['r'][1:len(val)]
val[0] = val[1]
r0 = np.linspace(0., 10., 1000)
pt_g = self._interp(val) #* np.sqrt(4.0 * np.pi)
sqrnorm = (pt_g**2 * self.rgd.dr_g).sum()
self.pt_jg.append(pt_g)
else:
self.l_j = [0]
gcut = self.rgd.r2g(1.0)
self.pt_jg = [np.zeros(gcut)] # XXX yet another "null" function
self.rcgauss = 0.0 # XXX .... what is this used for?
self.ni = sum([2 * l + 1 for l in self.l_j])
self.filename = None # remember filename?
self.fingerprint = None # XXX hexdigest the file?
self.HubU = None # XXX
self.lq = None # XXX
#if data['states']:
# states_lmax = max([state.l for state in data['states']])
#else:
# states_lmax = 1 # XXXX
if data['states']:
states_lmax = max([state.l for state in data['states']])
f_ln = [[] for _ in range(1 + states_lmax)]
electroncount = 0.0
for state in data['states']:
# Where should the electrons be in the inner list??
# This is probably wrong and will lead to bad initialization
f_ln[state.l].append(state.occupation)
electroncount += state.occupation
# The Cl.pz-hgh.UPF from quantum espresso has only 6
# but should have 7 electrons. Oh well....
err = abs(electroncount - self.Nv)
self.f_j = [state.occupation for state in data['states']]
self.n_j = [state.n for state in data['states']]
self.l_orb_j = [state.l for state in data['states']]
self.f_ln = f_ln
else:
self.n_j, self.l_orb_j, self.f_j, self.f_ln = \
figure_out_valence_states(self)
vlocal_unscreened = data['vlocal']
vbar_g, ghat_g = screen_potential(data['r'], vlocal_unscreened,
self.Nv)
self.vbar_g = self._interp(vbar_g) * np.sqrt(4.0 * np.pi)
self.ghat_lg = [4.0 * np.pi / self.Nv * self._interp(ghat_g)]
def __init__(self, data):
# data can be string (filename)
# or dict (that's what we are looking for).
# Maybe just a symbol would also be fine if we know the
# filename to look for.
if isinstance(data, basestring):
data = parse_upf(data)
assert isinstance(data, dict)
self.data = data # more or less "raw" data from the file
self.name = 'upf'
header = data['header']
keys = header.keys()
keys.sort()
self.symbol = header['element']
self.Z = atomic_numbers[self.symbol]
self.Nv = header['z_valence']
self.Nc = self.Z - self.Nv
self.Delta0 = -self.Nv / np.sqrt(4.0 * np.pi) # like hgh
self.rcut_j = [
data['r'][len(proj.values) - 1] for proj in data['projectors']
]
#beta = 0.1 # XXX nice parameters?
#N = 4 * 450 # XXX
# This is "stolen" from hgh. Figure out something reasonable
#rgd = AERadialGridDescriptor(beta / N, 1.0 / N, N,
# default_spline_points=100)
from gpaw.atom.radialgd import EquidistantRadialGridDescriptor
rgd = EquidistantRadialGridDescriptor(0.02)
self.rgd = rgd
# Whyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy???
# What abominable part of the code requires the states
# to be ordered like this?
self.jargs = self.get_jargs()
projectors = [data['projectors'][jarg] for jarg in self.jargs]
if projectors:
self.l_j = [proj.l for proj in projectors]
self.pt_jg = []
for proj in projectors:
val = proj.values.copy()
val /= 2.
val[1:] /= data['r'][1:len(val)]
val[0] = val[1]
pt_g = self._interp(val) #* np.sqrt(4.0 * np.pi)
#sqrnorm = (pt_g**2 * self.rgd.dr_g).sum()
self.pt_jg.append(pt_g)
else:
self.l_j = [0]
gcut = self.rgd.r2g(1.0)
self.pt_jg = [np.zeros(gcut)] # XXX yet another "null" function
self.rcgauss = 0.0 # XXX .... what is this used for?
self.ni = sum([2 * l + 1 for l in self.l_j])
self.filename = None # remember filename?
self.fingerprint = None # XXX hexdigest the file?
self.HubU = None # XXX
self.lq = None # XXX
#if data['states']:
# states_lmax = max([state.l for state in data['states']])
#else:
# states_lmax = 1 # XXXX
if data['states']:
states_lmax = max([state.l for state in data['states']])
f_ln = [[] for _ in range(1 + states_lmax)]
electroncount = 0.0
for state in data['states']:
# Where should the electrons be in the inner list??
# This is probably wrong and will lead to bad initialization
f_ln[state.l].append(state.occupation)
electroncount += state.occupation
# The Cl.pz-hgh.UPF from quantum espresso has only 6
# but should have 7 electrons. Oh well....
#err = abs(electroncount - self.Nv)
self.f_j = [state.occupation for state in data['states']]
self.n_j = [state.n for state in data['states']]
self.l_orb_j = [state.l for state in data['states']]
self.f_ln = f_ln
else:
self.n_j, self.l_orb_j, self.f_j, self.f_ln = \
figure_out_valence_states(self)
vlocal_unscreened = data['vlocal']
# The UPF representation of HGH setups should be equal to that
# used with setups='hgh'. But the UPF files do not contain
# info on the localization of the compensation charges! That
# means the screen_potential code will choose the shape of the
# compensation charges, resulting in some numerical differences.
#
# One could hack that it looks up some radii to compare e.g. H2O.
# The results of the below comments still have some numerical error.
# But it's not huge.
#a = None
#if self.symbol == 'H':
# a = 0.2
#elif self.symbol == 'O':
# a = .247621
vbar_g, ghat_g = screen_potential(data['r'], vlocal_unscreened,
self.Nv) #, a=a)
self.vbar_g = self._interp(vbar_g) * np.sqrt(4.0 * np.pi)
self.ghat_lg = [4.0 * np.pi / self.Nv * self._interp(ghat_g)]
def upfplot(setup, show=True):
# 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, psi, label='wf%d %s' % (j, st.label))
r, rho = rtrunc(pp['rhoatom'], 2)
wfsax.plot(r, rho, label='rho')
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('WF / density')
rhoax.set_ylabel('Comp charges')
fig.subplots_adjust(wspace=0.3)
if show:
pl.show()
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()