def read_runner(fileobj, index=-1):
"""
Read from a file in RuNNer format
index is the frame to read, default is last frame (index=-1).
"""
if isinstance(fileobj, str):
fileobj = open(fileobj)
if not isinstance(index, int) and not isinstance(index, slice):
raise TypeError('Index argument is neither slice nor integer!')
# If possible, build a partial index up to the last frame required
last_frame = None
if isinstance(index, int) and index >= 0:
last_frame = index
elif isinstance(index, slice):
if index.stop is not None and index.stop >= 0:
last_frame = index.stop
# scan through file to find where the frames start
fileobj.seek(0)
frames = []
natoms = 0
while fileobj:
line = fileobj.readline()
if line.strip() == '':
break
elif line.strip() == 'begin':
frame_pos = fileobj.tell()
elif line.split()[0] == 'atom':
natoms += 1
elif line.strip() == 'end':
frames.append((frame_pos, natoms))
natoms = 0
if last_frame is not None and len(frames) > last_frame:
break
if isinstance(index, int):
if index < 0:
tmpsnp = len(frames) + index
trbl = list(range(tmpsnp, tmpsnp + 1, 1))
else:
trbl = list(range(index, index + 1, 1))
elif isinstance(index, slice):
start = index.start
stop = index.stop
step = index.step
if start is None:
start = 0
elif start < 0:
start = len(frames) + start
if step is None:
step = 1
if stop is None:
stop = len(frames)
elif stop < 0:
stop = len(frames) + stop
trbl = list(range(start, stop, step))
if step < 0:
trbl.reverse()
for index in trbl:
frame_pos, natoms = frames[index]
fileobj.seek(frame_pos)
# comment line
comment_line = fileobj.readline().strip()
# Is there any valuable info to strip from the comment line?
# Is the comment line always present?
# info = key_val_str_to_dict(line)
info = {}
arrays = {}
cell = [
] # Now we have to read 3 lines to extract information about the lattice
for ln in range(3):
line = fileobj.readline()
vals = line.split()
cell.append(vals[1:4])
cell = np.array(
cell,
dtype='float') * units.Bohr # This should convert to Angstrom
positions = []
symbols = []
forces = []
numbers = []
for ln in range(natoms):
line = fileobj.readline()
vals = line.split()
coords = tuple([float(val) for val in vals[1:4]])
tmpforces = tuple([float(val) for val in vals[7:]])
symbols.append(vals[4])
positions.append(coords)
forces.append(tmpforces)
try:
positions = np.array(positions) * units.Bohr
forces = np.array(
forces
) * units.Hartree / units.Bohr # Transform from Ha/bohr to eV/angstrom
except TypeError:
raise IOError('Badly formatted data, ' +
'or end of file reached before end of frame')
line = fileobj.readline()
energy = float(line.split()[1])
line = fileobj.readline()
charge = float(line.split()[1])
arrays['forces'] = forces
info['nrg'] = energy
structure = Atoms(symbols=symbols,
positions=positions,
cell=cell,
pbc=True)
calc = SinglePointCalculator(structure, energy=energy, forces=forces)
structure.set_calculator(calc)
structure.comment = comment_line
#atoms = Atoms(symbols=symbols,
# positions=positions,
# cell=cell,
# pbc=pbc,
# info=info)
yield structure
