def _get_standardized_compressed_wfcs(atomconfig, wavecomp_result):
wavefuncs = []
waves_found_for_shell = {}
for nn, ll in atomconfig.valenceshells:
wfc012 = wavecomp_result.get_wavefunction(nn, ll)
wfc0_data = wfc012.data[:,0]
wfc0_grid = wfc012.grid
norm = wfc0_grid.dot(wfc0_data, wfc0_data)
logger.debug("Norm for wavefunc {:d}{:s}: {:f}".format(
nn, sc.ANGMOM_TO_SHELL[ll], norm))
wfc0 = soc.GridData(wfc0_grid, wfc0_data)
sign = get_normalized_sign(nn, ll, wfc0)
logger.debug("Sign for wavefunc {:d}{:s}: {:.1f}".format(
nn, sc.ANGMOM_TO_SHELL[ll], sign))
wfc012.data *= sign
previous_wfcs = waves_found_for_shell.get(ll, [])
if len(previous_wfcs):
coeffs = get_expansion_coefficients(wfc012, previous_wfcs)
msg = "Expansion coeffs of previous wavefuncs:"
msg += " {:f}" * len(coeffs)
logger.debug(msg.format(*coeffs))
wfc012 = orthogonalize_wave_and_derivatives(
wfc012, previous_wfcs, coeffs)
newwave = ( nn, ll, wfc012 )
if ll in waves_found_for_shell:
waves_found_for_shell[ll].append(newwave)
else:
waves_found_for_shell[ll] = newwave
wavefuncs.append(newwave)
return wavefuncs
def get_wavefunction012(self, ss, nn, ll):
"""Returns radial wave function and its first and second derivatives.
Returns
-------
density : GridData
Grid data with the wavefunction and its first and second derivatives.
"""
if ss == 0:
formstr = "wave_{:02d}{:s}_up.dat"
else:
formstr = "wave_{:02d}{:s}_dn.dat"
wavefile = formstr.format(nn, sc.ANGMOM_TO_SHELL[ll])
wavefile = os.path.join(self._workdir, wavefile)
if not os.path.exists(wavefile):
raise sc.SkgenException("Missing wave function file " + wavefile)
fp = open(wavefile, "r")
fp.readline()
fp.readline()
ngrid = int(fp.readline())
fp.readline()
# noinspection PyNoneFunctionAssignment,PyTypeChecker
wavefunc = np.fromfile(fp, dtype=float, count=5 * ngrid, sep=" ")
wavefunc.shape = (ngrid, 5)
grid = oc.RadialGrid(wavefunc[:, 0], wavefunc[:, 1])
wfcs = wavefunc[:, 2:5]
return oc.GridData(grid, wfcs)
def orthogonalize_wave_and_derivatives(wavefunc, prev_wavefuncs, coeffs):
if len(prev_wavefuncs) == 0:
return wavefunc
wfcnew_data = wavefunc.data.copy()
for coeff, wfcprev in zip(coeffs, prev_wavefuncs):
wfcnew_data -= coeff * wfcprev.data
norm = wavefunc.grid.dot(wfcnew_data[:,0], wfcnew_data[:,0])
wfcnew_data /= norm
return soc.GridData(wavefunc.grid, wfcnew_data)
def _store_potentials(workdir, potentials, iatom):
fname = "potentials{:d}.dat".format(iatom)
# Vxc up and down should be equivalent, twocnt reads only one.
newdata = potentials.data.take(
(radial_grid.VNUC, radial_grid.VHARTREE, radial_grid.VXCUP),
axis=1)
newgriddata = radial_grid.GridData(potentials.grid, newdata)
newgriddata.tofile(os.path.join(workdir, fname))
return fname
def get_potentials(self):
"""Returns various potential components of the atom
Returns
-------
potentials : GridData
Grid data with following potentials:
nuclear, coulomb, xc-spinup, xc-spindown.
"""
fp = open(os.path.join(self._workdir, "pot.dat"), "r")
fp.readline()
fp.readline()
ngrid = int(fp.readline())
# noinspection PyNoneFunctionAssignment,PyTypeChecker
pots = np.fromfile(fp, dtype=float, count=ngrid * 6, sep=" ")
fp.close()
pots.shape = (ngrid, 6)
grid = oc.RadialGrid(pots[:, 0], pots[:, 1])
potentials = pots[:, 2:6]
return oc.GridData(grid, potentials)
def _get_standardized_compressed_dens_wfcs(atomconfig, wavecomp_result):
wavefuncs = []
for qn, _ in atomconfig.occshells:
nn = qn[0]
ll = qn[1]
wfc012 = wavecomp_result.get_dens_wavefunction(nn, ll)
wfc0_data = wfc012.data[:, 0]
wfc0_grid = wfc012.grid
norm = wfc0_grid.dot(wfc0_data, wfc0_data)
logger.debug("Norm for wavefunc {:d}{:s}: {:f}".format(
nn, sc.ANGMOM_TO_SHELL[ll], norm))
wfc0 = soc.GridData(wfc0_grid, wfc0_data)
sign = get_normalized_sign(nn, ll, wfc0)
logger.debug("Sign for wavefunc {:d}{:s}: {:.1f}".format(
nn, sc.ANGMOM_TO_SHELL[ll], sign))
wfc012.data *= sign
newwave = (nn, ll, wfc012)
wavefuncs.append(newwave)
return wavefuncs
def get_density012(self):
"""Returns the radial density and its first and second derivatives.
Returns
-------
density : GridData
Grid data with the density and its first and second derivatives.
"""
fp = open(os.path.join(self._workdir, "dens.dat"), "r")
fp.readline()
fp.readline()
fp.readline()
fp.readline()
fp.readline()
ngrid = int(fp.readline())
# noinspection PyNoneFunctionAssignment,PyTypeChecker
dens = np.fromfile(fp, dtype=float, count=ngrid * 7, sep=" ")
fp.close()
dens.shape = (ngrid, 7)
grid = oc.RadialGrid(dens[:, 0], dens[:, 1])
density = dens[:, 2:5]
return oc.GridData(grid, density)
