def read_xyz(f: io.TextIOWrapper):
n = int(next(f))
comment = next(f)
m = read_matrix(f, n)
symbols = m[:, 0]
positions = m[:, 1:4].astype(np.float64)
return comment, symbols, positions
def read_outcar_a_lattice(f):
skip_until(f, "VOLUME and BASIS-vectors are now :")
next(f)
next(f)
next(f)
next(f)
lattices = read_matrix(f, 3)
return lattices[:, 0:3].astype(np.float64)
def read_outcar_a_position_force(f, n):
skip_until(
f,
"POSITION TOTAL-FORCE (eV/Angst)"
)
next(f)
pf = read_matrix(f, n)
return pf[:, :3].astype(np.float64), pf[:, 3:6].astype(np.float64)
def read_a_results_tag(f: io.TextIOWrapper):
name, tds = next(f).split()
_, t, d, s = tds.split(":")
_ = int(d)
shape = tuple(map(int, s.split(",")))
if t == "real":
dtype = np.float64
else:
raise RuntimeError()
vec = read_matrix(f, int(np.ceil(np.prod(shape) / 3))).astype(dtype)
return name, vec.reshape(shape)
def read_poscar(f: io.TextIOWrapper):
"""system, cell, symbols, coordinate, selective"""
title = next(f).strip()
unit = float(next(f).strip())
cell = read_matrix(f, 3).astype(np.float64)
sym = next(f).split()
num = [int(w) for w in next(f).split()]
symbols = expand(num, sym)
selective, cartesian = read_poscar_switch(f)
ct = read_matrix(f, len(symbols))
if cartesian:
coordinate = ct[:, 0:3].astype(np.float64)
else:
coordinate = ct[:, 0:3].astype(np.float64) @ cell
if selective:
selectived = np.logical_or(ct[:, 3:6] == "T", ct[:, 3:6] == "t")
else:
# selectived = np.full((len(symbols), 3), True)]
selectived = None
return title, unit, cell * unit, symbols, coordinate * unit, selectived
def read_doscar(f: io.TextIOWrapper):
# pylint: disable=W0612
(number_of_ions_including_empty_spheres, number_of_ions, including_pdos,
NCDIJ) = map(int,
next(f).split())
(volume_of_unit_cell, la, lb, lc, POTIM) = map(float, next(f).split())
TEBEG = float(next(f))
next(f)
SYSTEM = next(f)
Emax, Emin, FEDOS, Efermi, _ = map(float, next(f).split())
NEDOS = int(FEDOS)
DOS = read_matrix(f, NEDOS).astype(np.float64)
if including_pdos:
PDOS = []
for _ in range(number_of_ions):
next(f)
PDOS.append(read_matrix(f, NEDOS).astype(np.float64))
PDOS = np.array(PDOS)
else:
PDOS = None
return Emax, Emin, NEDOS, Efermi, DOS, PDOS
def read_outcar_a_frequency(f: io.TextIOWrapper, n):
head = next(f).split()
if head[1] == "f":
body = head[3:]
im = False
elif head[1] == "f/i=":
body = head[2:]
im = True
else:
raise NotImplementedError()
energy = float(body[4]) * kayser
next(f)
pos_freq = read_matrix(f, n).astype(np.float64)
next(f)
return im, energy, pos_freq
def read_convvec(self, f):
self.convvec.append(read_matrix(f, 3).astype(np.float64) * angstrom)
return next(f).split()