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Allow reading of kweights from file when working with siesta #4

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Allow reading of kweights from file when working with siesta #4

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35 changes: 30 additions & 5 deletions scripts/write_wfk_nc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -215,6 +215,7 @@ def read_all(self):
evals = []
evecs = []
wfsx_kpts = []
wfsx_weights = []

def change_gauge(k, evec):
""" Change the eigenvector gauge """
Expand All @@ -230,17 +231,22 @@ def change_gauge(k, evec):
# Read wavefunctions and eigenvalues
for wfc in self.wfsx_sile.yield_eigenstate():
wfsx_kpts.append(wfc.info['k'])
wfsx_weights.append(wfc.info['weight'])
evals.append(wfc.c)
# To get the same eigvecs as eigh returns we need to transpose the
# array and change the gauge from 'r' to 'R'
evecs.append(change_gauge(wfc.info['k'], wfc.state).T)

wfsx_kpts = np.asarray(wfsx_kpts)
wfsx_weights = np.asarray(wfsx_weights)

# If any k-point occurs more than once in the WaveFuncKPoints block,
# we discard the duplicates
is_duplicate = self._is_duplicate(wfsx_kpts)
self.wfsx_kpts = wfsx_kpts[~is_duplicate]
self.wfsx_weights = wfsx_weights[~is_duplicate]
# Normalize weights
self.wfsx_weights /= np.sum(self.wfsx_weights)
self.evals = np.array(evals, dtype=float)[~is_duplicate]
if self.shift_fermi is not None:
self.evals += self.shift_fermi
Expand Down Expand Up @@ -293,8 +299,7 @@ def write_to_netcdf(self, fname):
root.variables["atomic_numbers"][:] = self.atoms.get_atomic_numbers()
root.variables["eigenvalues"][:] = self.evals
root.variables["kpts"][:] = self.wfsx_kpts
root.variables["kweights"][:] = np.ones(
nkpt, dtype=float)/nkpt
root.variables["kweights"][:] = self.wfsx_weights
# print(self.orbs)
# print(len(self.orbs))
#root.variables["orb_names"][:] = self.orbs
Expand Down Expand Up @@ -351,9 +356,20 @@ def find_all(self, kpts):
# Define alias for find_all to unify in wrapper's interface
solve_all = find_all

def set_kweights(self, kpts, kweights):

kpts = np.asarray(kpts)
sort_idx = np.where(
np.all(np.isclose(self.wfsx_kpts[None, :], kpts[:, None]),
axis=-1))[1]
print(self.wfsx_weights)
print(self.wfsx_weights[sort_idx])
self.wfsx_weights[sort_idx] = kweights


def write_to_netcdf(folder=None, spin="soc", fdf_fname="siesta.fdf",
wfxfname="siesta.fullBZ.WFSX", ncfname="wf.nc"):
wfxfname="siesta.fullBZ.WFSX", kwfname=None,
ncfname="wf.nc"):
if spin != "soc":
raise NotImplementedError("currently only spin=soc is implemented.")
from sisl.physics.spin import Spin
Expand All @@ -367,8 +383,17 @@ def write_to_netcdf(folder=None, spin="soc", fdf_fname="siesta.fdf",
efermi = fdf.read_fermi_level()
model = SislWFSXWrapper(geom, wfsx_sile, spin=Spin(spin),
ispin=None, shift_fermi=None)

if kwfname is not None:
tmp = np.genfromtxt(kwfname)
kpts = tmp[:,:3]
kweights = tmp[:,3]
model.set_kweights(kpts, kweights)

model.write_to_netcdf(ncfname)


write_to_netcdf(folder='./', fdf_fname='siesta.fdf',
wfxfname="siesta.fullBZ.WFSX", ncfname='wf.nc')
write_to_netcdf(folder='../siesta', fdf_fname='in.fdf',
wfxfname="../siesta/graphene.selected.WFSX",
kwfname='kpoints',
ncfname='wfk.nc')