def parse_kline(line, ik=None):
from qharv.reel import ascii_out
assert 'k(' in line
ikt, kvect, wkt = line.split('=')
myik = int(ascii_out.lr_mark(ikt, '(', ')'))
if ik is not None: # check k index
assert ik == myik - 1 # fortran 1-based indexing
wk = float(wkt)
klist = ascii_out.lr_mark(kvect, '(', ')').split()
kvec = np.array(klist, dtype=float)
return kvec, wk
def read_out_cell(scf_out, ndim=3):
axes = np.zeros([ndim, ndim])
from qharv.reel import ascii_out
mm = ascii_out.read(scf_out)
idx = mm.find(b'crystal axes')
mm.seek(idx)
mm.readline()
for idim in range(ndim):
line = mm.readline()
right = line.split('=')[-1]
text = ascii_out.lr_mark(right, '(', ')')
axes[idim, :] = map(float, text.split())
return axes
def get_supertwists(qmc_out):
""" read supercell twists from QMCPACK output
Args:
qmc_out (str): QMCPACK output, must contain "Super twist #"
Return:
np.array: an array of twist vectors (ntwist, ndim)
"""
from qharv.reel import ascii_out
mm = ascii_out.read(qmc_out)
idxl = ascii_out.all_lines_with_tag(mm, 'Super twist #')
lines = ascii_out.all_lines_at_idx(mm, idxl)
data = []
for line in lines:
text = ascii_out.lr_mark(line, '[', ']')
vec = np.array(text.split(), dtype=float)
data.append(vec)
mat = np.array(data)
return mat
def retrieve_occupations(nscf_outfile, max_nbnd_lines=10):
""" read the eigenvalues and occupations of DFT orbitals at every available kpoint in an non-scf output produced by pwscf """
from qharv.reel import ascii_out
span = 7
def scanf_7f(line, n):
""" implement scanf("%7.*f") """
numl = []
for i in range(n):
token = line[span * i:span * (i + 1)]
num = float(token)
numl.append(num)
return numl
fhandle = open(nscf_outfile, 'r+')
mm = mmap(fhandle.fileno(), 0)
# read number of k points
nk_prefix = b"number of k points="
idx = mm.find(nk_prefix)
mm.seek(idx)
nk_line = mm.readline()
nk = int(nk_line.strip(nk_prefix).split()[0])
# skip to the end of band structure calculation
idx = mm.find(b'End of self-consistent calculation')
idx = mm.find(b'End of band structure calculation')
mm.seek(idx)
# read the eigenvalues and occupations at each kpoint
kpt_prefix = "k ="
data = []
for ik in range(nk):
idx = mm.find(kpt_prefix.encode())
mm.seek(idx)
kpt_line = mm.readline()
kxkykz = ascii_out.lr_mark(kpt_line, '=', '(')
kpt = scanf_7f(kxkykz, 3)
mm.readline() # skip empty line
eval_arr = np.array([])
for iline in range(max_nbnd_lines):
tokens = mm.readline().split()
if len(tokens) == 0:
break
# end if
eval_arr = np.append(eval_arr, map(float, tokens))
# end for iline
idx = mm.find(b'occupation numbers')
mm.seek(idx)
mm.readline() # skip current line
occ_arr = np.array([])
for iline in range(100):
tokens = mm.readline().split()
if len(tokens) == 0:
break
# end if
occ_arr = np.append(occ_arr, map(float, tokens))
# end for iline
entry = {
'ik': ik,
'kpt': list(kpt),
'eval': list(eval_arr),
'occ': list(occ_arr)
}
data.append(entry)
# end for
mm.close()
fhandle.close()
return data
def parse_nscf_bands(nscf_out, span=7, trailer='occupation numbers'):
data = {} # build a dictionary as return value
def scanf_7f(line, n):
""" implement scanf("%7.*f") """
numl = []
for i in range(n):
token = line[span * i:span * (i + 1)]
num = float(token)
numl.append(num)
return numl
def parse_float_body(body):
""" parse a blob of floats """
lines = body.split('\n')
numl = []
for line in lines:
if len(line) == 0: continue
numl += map(float, line.split())
return numl
from qharv.reel import ascii_out
ndim = 3
mm = ascii_out.read(nscf_out)
alat = ascii_out.name_sep_val(mm, 'lattice parameter (alat)')
blat = 2 * np.pi / alat
# find the beginnings of each band
bhead = ' k ='
idxl = ascii_out.all_lines_with_tag(mm, bhead)
nkpt = len(idxl)
data['nkpt'] = nkpt
# estimate the end of the last band
idx1 = ascii_out.all_lines_with_tag(mm, trailer)[-1]
# trick to use no if statement in the loop
idxl = idxl + [idx1]
kvecs = [] # (nkpt, ndim)
mat = [] # (nkpt, nbnd)
for ikpt in range(nkpt):
# specify beginning and end of the band output
idx0 = idxl[ikpt]
idx1 = idxl[ikpt + 1]
# parse band output
# first read header
mm.seek(idx0)
header = mm.readline().decode()
if not 'bands (ev)' in header: continue
kxkykz = ascii_out.lr_mark(header, '=', '(')
kvec = scanf_7f(kxkykz, ndim)
kvecs.append(kvec)
# then read body
body = mm[mm.tell():idx1].decode().strip('\n')
if trailer in body:
idx2 = mm.find(trailer.encode())
body = mm[mm.tell():idx2].strip('\n')
row = parse_float_body(body)
mat.append(row)
# end for ikpt
data['kvecs'] = blat * np.array(kvecs)
data['bands'] = np.array(mat)
return data
def read_sym_ops(scf_out, ndim=3):
""" read symmetry operators
Args:
scf_out (str): QE output file
ndim (int, optional): number of spatial dimensions, default is 3
Return:
list: all symmetry operators, each is represented as a dictionary
isym is index, name is description, vec is shift, mat is rotation
"""
from qharv.reel import ascii_out
mm = ascii_out.read(scf_out)
# find starting location of symmetry operator output
idx = mm.find(b'Sym. Ops.')
if idx == -1:
msg = 'no symmetry operations printed in %s. Is verbosity high?' % scf_out
raise RuntimeError(msg)
# rewind to beginning of line
idx0 = mm.rfind(b'\n', 0, idx)
mm.seek(idx0 + 1)
header = mm.readline().decode()
nsym = int(header.split()[0])
# check the number of symmetry outputs
idxl = ascii_out.all_lines_with_tag(mm, 'isym = ')
if len(idxl) != nsym:
raise RuntimeError('found %d symm. expected %d' % (len(idxl), nsym))
# parse symmetry operators
symops = []
for idx in idxl:
mm.seek(idx)
# read symmetry index and name: isym, name
line0 = mm.readline().decode()
text0 = line0.split('=')[1]
tokens0 = text0.split()
isym = int(tokens0[0])
name = ' '.join(tokens0[1:])
# read translation vector: vec
vec = [0] * ndim
if 'cart. axis' in name:
vect = ascii_out.lr_mark(line0, '[', ']')
vec[:] = list(map(float, vect.split(',')))
# read rotation matrix: mat
mat = []
idx = mm.find(b'cryst.')
mm.readline() # skip empty line
for idim in range(ndim):
line = mm.readline().decode()
if 'cryst.' in line:
line = line.split('=')[1]
text = ascii_out.lr_mark(line, '(', ')')
mat.append(list(map(float, text.split())))
entry = {'isym': isym, 'name': name, 'vec': vec, 'mat': mat}
symops.append(entry)
mm.close()
return symops