def from_string(header_str):
"""
Reads Header string and returns Header object if header was
generated by pymatgen.
Args:
header_str:
pymatgen generated feff.inp header
Returns:
structure object.
"""
lines = tuple(clean_lines(header_str.split("\n"), False))
comment = lines[0]
feffpmg = comment.find("pymatgen")
if feffpmg > 0:
source = lines[1].split()[2]
natoms = int(lines[7].split()[2])
basis_vec = lines[5].split()
a = float(basis_vec[2])
b = float(basis_vec[3])
c = float(basis_vec[4])
lengths = [a, b, c]
basis_ang = lines[6].split()
alpha = float(basis_ang[2])
beta = float(basis_ang[3])
gamma = float(basis_ang[4])
angles = [alpha, beta, gamma]
lattice = Lattice.from_lengths_and_angles(lengths, angles)
atomic_symbols = []
for i in xrange(8, 8 + natoms):
atomic_symbols.append(lines[i].split()[2])
# read the atomic coordinates
coords = []
for i in xrange(natoms):
toks = lines[i + 8].split()
coords.append([float(s) for s in toks[3:]])
struct_fromfile = Structure(lattice, atomic_symbols, coords, False,
False, False)
struct_fromfile.compound = lines[3].split()[2]
h = Header(struct_fromfile, comment)
h.set_source(source)
return h
else:
return "Header not generated by pymatgen, " \
"cannot return header object"
