def tofile(self, fobj, relcoords=False):
"""Writes a GEN file.
Args:
fobj: File name or file object where geometry should be written.
relcoords: If true, geometry will be outputted in relative
coordinates (as multiples of the lattice vectors)
"""
fp = openfile(fobj, "w")
line = [ "{0:d}".format(self.geometry.natom), ]
geo = self.geometry
if geo.periodic:
if relcoords:
line.append("F")
coords = geo.relcoords
else:
line.append("S")
coords = geo.coords
else:
line.append("C")
coords = geo.coords
fp.write(" ".join(line) + "\n")
fp.write(" ".join(geo.specienames) + "\n")
for ii in range(geo.natom):
fp.write("{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:
fp.write("{0:18.10E} {1:18.10E} {2:18.10E}\n".format(*geo.origin))
for vec in geo.latvecs:
fp.write("{0:18.10E} {1:18.10E} {2:18.10E}\n".format(*vec))
fp.close()
def fromfile(cls, fobj):
"""Creates an XYZ instance from a file.
Args:
fobj: filename or file like object containing geometry in
XYZ-format.
"""
fp = openfile(fobj, "r")
lines = fp.readlines()
fp.close()
words = lines[0].split()
natom = int(words[0])
comment = lines[1].strip()
specienames = []
speciedict = {}
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()
species = words[0]
index = speciedict.get(species, -1)
if index == -1:
specienames.append(species)
speciedict[species] = len(specienames) - 1
indexes[ii] = len(specienames) - 1
else:
indexes[ii] = index
coords[ii] = np.array(words[1:4], dtype=float)
geometry = Geometry(specienames, indexes, coords)
return cls(geometry, comment)
def fromfile(cls, fobj):
"""Returns a band.out representation created from a file object.
Args:
fobj: File like object or string with file name.
"""
fp = openfile(fobj)
txt = fp.read()
fp.close()
ispins = set()
kweights = []
eigvalarrays = []
match = PAT_BLOCK.search(txt)
while match:
ispins.add(int(match.group("ispin")))
kweight = match.group("kweight")
if kweight:
kweights.append(float(kweight))
else:
kweights.append(1.0)
tmp = np.array(match.group("vals").split(), dtype=float)
eigvalarrays.append(tmp.reshape((-1, 2)))
match = PAT_BLOCK.search(txt, match.end())
nspin = len(ispins)
nkpt = len(eigvalarrays) / nspin
eigvalspin = np.array(eigvalarrays).reshape((nspin, nkpt, -1, 2))
kweights = np.array(kweights).reshape((nspin, nkpt))
return cls(kweights, eigvalspin)
def fromfile(cls, fobj):
"""Returns a band.out representation created from a file object.
Args:
fobj: File like object or string with file name.
"""
fp = openfile(fobj)
txt = fp.read()
fp.close()
ispins = set()
kweights = []
eigvalarrays = []
match = PAT_BLOCK.search(txt)
while match:
ispins.add(int(match.group("ispin")))
kweight = match.group("kweight")
if kweight:
kweights.append(float(kweight))
else:
kweights.append(1.0)
tmp = np.array(match.group("vals").split(), dtype=float)
eigvalarrays.append(tmp.reshape((-1, 2)))
match = PAT_BLOCK.search(txt, match.end())
nspin = len(ispins)
nkpt = len(eigvalarrays) / nspin
eigvalspin = np.array(eigvalarrays).reshape((nspin, nkpt, -1, 2))
kweights = np.array(kweights).reshape((nspin, nkpt))
return cls(kweights, eigvalspin)
def tofile(self, fobj, relcoords=False):
"""Writes a GEN file.
Args:
fobj: File name or file object where geometry should be written.
relcoords: If true, geometry will be outputted in relative
coordinates (as multiples of the lattice vectors)
"""
fp = openfile(fobj, "w")
line = [
"{0:d}".format(self.geometry.natom),
]
geo = self.geometry
if geo.periodic:
if relcoords:
line.append("F")
coords = geo.relcoords
else:
line.append("S")
coords = geo.coords
else:
line.append("C")
coords = geo.coords
fp.write(" ".join(line) + "\n")
fp.write(" ".join(geo.specienames) + "\n")
for ii in range(geo.natom):
fp.write("{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:
fp.write("{0:18.10E} {1:18.10E} {2:18.10E}\n".format(*geo.origin))
for vec in geo.latvecs:
fp.write("{0:18.10E} {1:18.10E} {2:18.10E}\n".format(*vec))
fp.close()
def fromfile(cls, fobj):
"""Creates an XYZ instance from a file.
Args:
fobj: filename or file like object containing geometry in
XYZ-format.
"""
fp = openfile(fobj, "r")
lines = fp.readlines()
fp.close()
words = lines[0].split()
natom = int(words[0])
comment = lines[1].strip()
specienames = []
speciedict = {}
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()
species = words[0]
index = speciedict.get(species, -1)
if index == -1:
specienames.append(species)
speciedict[species] = len(specienames) - 1
indexes[ii] = len(specienames) - 1
else:
indexes[ii] = index
coords[ii] = np.array(words[1:4], dtype=float)
geometry = Geometry(specienames, indexes, coords)
return cls(geometry, comment)
def fromfile(cls, fobj):
'''Reads crystallographic information from a CIF file.
Args:
fobj: filename or file like object containing geometry in
CIF-format.
'''
fp = openfile(fobj, "r")
lines = fp.readlines()
fp.close()
celllengths = np.empty(3, dtype=float)
cellangles = np.empty(3, dtype=float)
for jj in range(3):
celllengths[jj] = lines[jj + 1].split()[1]
cellangles[jj] = lines[jj + 4].split()[1]
natom = len(lines) - 13
specienames = []
speciedict = {}
indexes = np.empty((natom, ), dtype=int)
coords = np.empty((natom, 3), dtype=float)
for ii, line in enumerate(lines[13:13+natom]):
words = line.split()
species = words[0]
index = speciedict.get(species, -1)
if index == -1:
specienames.append(species)
speciedict[species] = len(specienames) - 1
indexes[ii] = len(specienames) - 1
else:
indexes[ii] = index
coords[ii] = np.array(words[1:4], dtype=float)
latvecs = get_latvecs_fromcif(celllengths, cellangles)
geometry = Geometry(specienames, indexes, coords, latvecs=latvecs, relcoords=True)
return cls(geometry)
def tofile(self, fobj):
"""Writes an XYZ file.
Args:
fobj: File name or file object where geometry should be written.
"""
fp = openfile(fobj, "w")
geo = self.geometry
fp.write("{0:d}\n".format(geo.natom))
fp.write(self.comment + "\n")
for ii in range(geo.natom):
fp.write("{0:3s} {1:18.10E} {2:18.10E} {3:18.10E}\n".format(
geo.specienames[geo.indexes[ii]], *geo.coords[ii]))
fp.close()
def tofile(self, fobj):
"""Writes an XYZ file.
Args:
fobj: File name or file object where geometry should be written.
"""
fp = openfile(fobj, "w")
geo = self.geometry
fp.write("{0:d}\n".format(geo.natom))
fp.write(self.comment + "\n")
for ii in range(geo.natom):
fp.write("{0:3s} {1:18.10E} {2:18.10E} {3:18.10E}\n".format(
geo.specienames[geo.indexes[ii]], *geo.coords[ii]))
fp.close()
def tofile(self, fobj):
geo = self.geometry
fp = openfile(fobj, "w")
fp.write("data_global\n")
for name, value in zip(["a", "b", "c"], self.celllengths):
fp.write("_cell_length_{0:s} {1:.10f}\n".format(name, value))
# cell angles are needed in degrees
for name, value in zip(["alpha", "beta", "gamma"],
self.cellangles * 180.0 / np.pi):
fp.write("_cell_angle_{0:s} {1:.10f}\n".format(name, value))
fp.write("_symmetry_space_group_name_H-M 'P 1'\n")
fp.write("loop_\n_atom_site_label\n_atom_site_fract_x\n"
"_atom_site_fract_y\n_atom_site_fract_z\n")
for ii in range(geo.natom):
fp.write("{0:3s} {1:.10f} {2:.10f} {3:.10f}\n".format(
geo.specienames[geo.indexes[ii]], *geo.relcoords[ii]))
fp.close()
def tofile(self, fobj):
geo = self.geometry
fp = openfile(fobj, "w")
fp.write("data_global\n")
for name, value in zip(["a", "b", "c"], self.celllengths):
fp.write("_cell_length_{0:s} {1:.10f}\n".format(name, value))
# cell angles are needed in degrees
for name, value in zip(["alpha", "beta", "gamma"],
self.cellangles * 180.0 / np.pi):
fp.write("_cell_angle_{0:s} {1:.10f}\n".format(name, value))
fp.write("_symmetry_space_group_name_H-M 'P 1'\n")
fp.write("loop_\n_atom_site_label\n_atom_site_fract_x\n"
"_atom_site_fract_y\n_atom_site_fract_z\n")
for ii in range(geo.natom):
fp.write("{0:3s} {1:.10f} {2:.10f} {3:.10f}\n".format(
geo.specienames[geo.indexes[ii]], *geo.relcoords[ii]))
fp.close()
def fromfile(cls, fobj):
"""Returns a band.out representation created from a file object.
Args:
fobj: File like object or string with file name.
"""
fp = openfile(fobj)
txt = fp.read()
fp.close()
ispins = set()
kweights = []
eigvalarrays = []
match = _PAT_BLOCK.search(txt)
while match:
ispin = match.group("ispin")
if ispin:
ispins.add(int(ispin))
else:
ispins.add(1)
kweight = match.group("kweight")
if kweight:
kweights.append(float(kweight))
else:
kweights.append(1.0)
vals = match.group("vals")
tmp = np.array(vals.split(), dtype=float)
# Only keep last two data columns
# (optional first column, if present, contains sequential numbering)
nrows = vals.strip().count('\n') + 1
ncols = len(tmp) // nrows
tmp.shape = (nrows, ncols)
tmp = tmp[:, ncols - 2:ncols]
eigvalarrays.append(tmp)
match = _PAT_BLOCK.search(txt, match.end())
nspin = len(ispins)
nkpt = len(eigvalarrays) // nspin
eigvalspin = np.array(eigvalarrays)
eigvalspin.shape = (nspin, nkpt, -1, 2)
kweights = np.array(kweights)
kweights.shape = (nspin, nkpt)
return cls(kweights, eigvalspin)
def fromfile(cls, fobj):
"""Creates a Gen instance from a file.
Args:
fobj: filename or file like object containing geometry in
GEN-format.
"""
fp = openfile(fobj, "r")
lines = fp.readlines()
fp.close()
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)
def fromfile(cls, fobj):
"""Creates a Gen instance from a file.
Args:
fobj: filename or file like object containing geometry in
GEN-format.
"""
fp = openfile(fobj, "r")
lines = fp.readlines()
fp.close()
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)