def tofile(self, fobj):
"""Writes a GEN file.
Args:
fobj: File name or file object where geometry should be written.
"""
lines = []
line = ["{0:d}".format(self.geometry.natom)]
geo = self.geometry
if geo.periodic:
if self.fractional:
line.append("F")
coords = geo.relcoords
else:
line.append("S")
coords = geo.coords
else:
line.append("C")
coords = geo.coords
coords = _round_to_zero(coords, _TOLERANCE)
lines.append(" ".join(line) + "\n")
lines.append(" ".join(geo.specienames) + "\n")
for ii in range(geo.natom):
lines.append("{0:6d} {1:3d} {2:18.10E} {3:18.10E} {4:18.10E}\n"\
.format(ii + 1, geo.indexes[ii] + 1, *coords[ii]))
if geo.periodic:
origin = _round_to_zero(geo.origin, _TOLERANCE)
lines.append("{0:18.10E} {1:18.10E} {2:18.10E}\n".format(*origin))
latvecs = _round_to_zero(geo.latvecs, _TOLERANCE)
for vec in latvecs:
lines.append("{0:18.10E} {1:18.10E} {2:18.10E}\n".format(*vec))
with OpenFile(fobj, 'w') as fp:
fp.writelines(lines)
def fromfile(cls, fobj):
"""Creates a Gen instance from a file.
Args:
fobj: filename or file like object containing geometry in
GEN-format.
"""
with OpenFile(fobj, 'r') as fp:
alllines = fp.readlines()
# strip out comments starting with hashmarks
lines = []
for line in alllines:
li = line.partition('#')[0]
li = li.rstrip()
if li:
lines.append(li)
words = lines[0].split()
natom = int(words[0])
flag = words[1].lower()
if flag == "s":
periodic = True
relative = False
elif flag == "f":
periodic = True
relative = True
else:
periodic = False
relative = False
specienames = lines[1].split()
indexes = np.empty((natom, ), dtype=int)
coords = np.empty((natom, 3), dtype=float)
for ii, line in enumerate(lines[2:2 + natom]):
words = line.split()
indexes[ii] = int(words[1]) - 1
coords[ii] = np.array(words[2:5], dtype=float)
if periodic:
origin = np.array(lines[natom + 2].split(), dtype=float)
latvecs = np.empty((3, 3), dtype=float)
for jj in range(3):
latvecs[jj] = np.array(lines[natom + 3 + jj].split(),
dtype=float)
else:
origin = None
latvecs = None
geometry = Geometry(specienames, indexes, coords, latvecs, origin,
relative)
return cls(geometry, relative)