def get_all_rhok(fwf, kbrags, norb=None, ispin=0, show_progress=True):
from qharv.seed import wf_h5
from qharv.inspect import axes_pos
from rsgub.grids.forlib.find_gvecs import calc_rhok
fp = wf_h5.read(fwf)
axes = wf_h5.get(fp, 'axes')
# calculate ukbrags
raxes = axes_pos.raxes(axes)
kcand = np.dot(kbrags, np.linalg.inv(raxes))
ukbrags = np.round(kcand).astype(int)
# check ukbrags
kbrags1 = np.dot(ukbrags, raxes)
assert np.allclose(kbrags, kbrags1)
# calculate rhok
gvecs = wf_h5.get(fp, 'gvectors')
ntwist = wf_h5.get(fp, 'nkpt')[ispin]
# store complex numbers in real view
data = np.zeros([ntwist, 2*len(ukbrags)])
if show_progress:
from progressbar import ProgressBar
bar = ProgressBar(maxval=ntwist)
for itwist in range(ntwist):
cmat = wf_h5.get_cmat(fp, itwist, ispin, norb=norb)
val = 2*calc_rhok(ukbrags, gvecs, cmat)
data[itwist, :] = val.view(float)
if show_progress:
bar.update(itwist)
fp.close()
return data
def get_momenta_and_weights(fp, ispin, ikpt, kmax, ecore, efermi):
""" Histogram psig^2 for a single determinant of Kohn-Sham orbitals at a
single twist. Select states with momenta k<kmax and energy ecore<e<efermi.
Args:
fp (h5py.File): pwscf.pwscf.h5 file pointer
ispin (int): determinant index (0: unpolarized, 0/1: polarized)
ikpt (int): twist vector index
kmax (float): maximum momentum to record
ecore (float): Core state energy bound. States below ecore are excluded
efermi (float): Fermi energy
Return:
(np.array, np.array): (momenta, weights)
"""
# get reciprocal lattice vectors to do lattice transformation
axes = wf_h5.get(fp, 'axes')
raxes = axes_pos.raxes(axes)
# Bloch function momenta (kvecs)
gvecs = wf_h5.get(fp, 'gvectors')
kvecs = np.dot(gvecs, raxes)
# crystal momentum (tvec)
kpath = wf_h5.kpoint_path(ikpt)
utvec = fp[os.path.join(kpath, 'reduced_k')].value
tvec = np.dot(utvec, raxes)
# true momentum = crystal + Bloch momentum
mykvecs = kvecs + tvec[np.newaxis, :]
# keep kvectors below kmax
mykmags = np.linalg.norm(mykvecs, axis=1)
sel = mykmags < kmax
momenta = mykvecs[sel]
# accumulate occupation
weights = np.zeros(len(momenta))
# keep states below the Fermi level and outside the core
nstate = fp[os.path.join(kpath, 'spin_%d' % ispin,
'number_of_states')].value[0]
evals = fp[os.path.join(kpath, 'spin_%d' % ispin, 'eigenvalues')].value
esel = (evals > ecore) & (evals < efermi)
states = np.arange(nstate)
for istate in states[esel]:
psig = wf_h5.get_orb_in_pw(fp, ikpt, ispin, istate)
pg2 = psig.conj() * psig
if not np.allclose(pg2.imag, 0): raise RuntimeError('dot not zero')
pg2 = pg2.real[sel]
weights += pg2
return momenta, weights
def write_detsk(h5file, ikpt, fwf, ispin, nsh0, kc):
"""Calculate determinant S(k) at given twist
Args:
h5file (tables.file.File): hdf5 file handle
ikpt (int): twist index
fwf (str): wf h5 file e.g. pwscf.pwscf.h5
ispin (int): spin index, use 0 for unpolarized
nsh0 (int): number of shells to use
kc (float): PW cutoff
"""
from qharv.seed import wf_h5
from qharv.inspect.axes_pos import raxes
from qharv.reel.config_h5 import save_dict
from solith.li_nofk.forlib.det import calc_detsk
from chiesa_correction import mirror_xyz, cubic_pos
# creat slab for twist
gname = 'twist%s' % str(ikpt).zfill(3)
slab = h5file.create_group('/', gname, '')
# read wf file
fp = wf_h5.read(fwf)
gvecs = wf_h5.get(fp, 'gvectors')
cmat = wf_h5.get_cmat(fp, ikpt, ispin)
wf_h5.normalize_cmat(cmat)
axes = wf_h5.get(fp, 'axes')
fp.close()
raxes = raxes(axes)
# decide which qvectors to calculate S(q)
qvecs = mirror_xyz(cubic_pos(nsh0))
kvecs = np.dot(qvecs, raxes)
kmags = np.linalg.norm(kvecs, axis=-1)
qsel = (1e-8 < kmags) & (kmags < kc)
# calculate S(k)
sk0 = calc_detsk(qvecs[qsel], gvecs, cmat)
# save
arr_dict = {
'raxes': raxes,
'gvecs': qvecs[qsel],
'sk0': sk0
}
save_dict(arr_dict, h5file, slab)
def get_det_nk(fp, efermi, ecore=-np.inf, kmax=np.inf, ispin=0):
"""Calculate momentum distribution from Kohn-Sham determinant
same as get_momentum_distribution, but faster
Args:
fp (h5py.File): pwscf.pwscf.h5 file pointer
efermi (float): Fermi energy
ecore (float, optional): core energy, default -np.inf
kmax (float, optional): maximum k magnitude to record, default np.inf
ispin (int, optiona): default 0
Return:
(np.array, np.array): (kvecs, nkm), kvectors and n(k) mean (no error)
"""
from solith.li_nofk.forlib.det import nofk
# need Kohn-Sham eigenvalues to decide which states to use
bands = wf_h5.get_bands(fp, ispin=ispin)
nt, nstate = bands.shape
# need kgrid info: basis (raxes), unshifted (kvecs0), twists (tvecs)
axes = wf_h5.get(fp, 'axes')
raxes = axes_pos.raxes(axes)
gvecs = wf_h5.get(fp, 'gvectors')
utvecs = wf_h5.get_twists(fp)
tvecs = np.dot(utvecs, raxes)
kvecs0 = np.dot(gvecs, raxes)
# calculate n(k) at each twist
kvecsl = []
nkml = []
for it in range(nt):
kvecs = kvecs0 + tvecs[it] # current twist
# histogram orb^2
cmat = wf_h5.get_cmat(fp, it, ispin, nstate)
nocc, npw = cmat.shape
weights = nofk(kvecs, cmat, bands[it], kmax, ecore, efermi)
# save within a cutoff
kmags = np.linalg.norm(kvecs, axis=-1)
sel = kmags < kmax
kvecsl.append(kvecs[sel])
nkml.append(weights[sel])
kvecs = np.concatenate(kvecsl, axis=0)
nkm = np.concatenate(nkml)
return kvecs, nkm
def get_rhok(fwf, kbrags, norb=None, itwist=0, ispin=0): from qharv.seed import wf_h5 from qharv.inspect import axes_pos from rsgub.grids.forlib.find_gvecs import calc_rhok fp = wf_h5.read(fwf) axes = wf_h5.get(fp, 'axes') gvecs = wf_h5.get(fp, 'gvectors') cmat = wf_h5.get_cmat(fp, itwist, ispin, norb=norb) fp.close() # calculate ukbrags raxes = axes_pos.raxes(axes) kcand = np.dot(kbrags, np.linalg.inv(raxes)) ukbrags = np.round(kcand).astype(int) # check ukbrags kbrags1 = np.dot(ukbrags, raxes) assert np.allclose(kbrags, kbrags1) # calculate rhok val = 2*calc_rhok(ukbrags, gvecs, cmat) return val
def get_momentum_distribution(fp, kmax, efermi, ispin=0, ecore=-np.inf):
""" obtain momentum distribution from Kohn-Sham determinant stored
in QMCPACK wf.h5 file format
Args:
fp (h5py.File): pwscf.pwscf.h5 file pointer
kmax (float): maximum k magnitude to record
efermi (float): Fermi energy
Return:
(np.array, np.array): (kvecs, nkm), kvectors and n(k) mean (no error)
"""
nkpt = wf_h5.get(fp, 'nkpt')[0]
mlist = []
wlist = []
for ikpt in range(nkpt):
momenta, weights = get_momenta_and_weights(fp, ispin, ikpt, kmax,
ecore, efermi)
mlist += momenta.tolist()
wlist += weights.tolist()
# end for ikpt
kvecs = np.array(mlist)
nkm = np.array(wlist)
return kvecs, nkm