def read_json(filedesc, **kwargs):
"""Reads a JSON-style file with i-pi style comments and creates an Atoms and Cell object.
Args:
filedesc: An open readable file object from a json formatted file with i-PI header comments.
Returns:
An Atoms object with the appropriate atom labels, masses and positions.
A Cell object.
"""
try:
line = json.loads(filedesc.readline())
except ValueError:
raise EOFError("The file descriptor hit EOF.")
atoms = Atoms(line[0])
atoms.q = np.asarray(line[8])
atoms.names = np.asarray(line[9], dtype='|S4')
atoms.m = np.asarray(map(Elements.mass, atoms.names))
a = float(line[1])
b = float(line[2])
c = float(line[3])
alpha = float(line[4]) * np.pi / 180
beta = float(line[5]) * np.pi / 180
gamma = float(line[6]) * np.pi / 180
h = mt.abc2h(a, b, c, alpha, beta, gamma)
cell = Cell(h)
return {"atoms": atoms, "cell": cell}
def read_pdb(filedesc):
"""Takes a pdb-style file and creates an Atoms and Cell object.
Args:
filedesc: An open readable file object from a pdb formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions,
and a Cell object with the appropriate cell dimensions and an estimate
of a reasonable cell mass.
"""
header = filedesc.readline()
if "TITLE" in header:
header = filedesc.readline() # skip the comment field
if header == "":
raise EOFError("End of file or empty header in PDB file")
a = float(header[6:15])
b = float(header[15:24])
c = float(header[24:33])
alpha = float(header[33:40])
beta = float(header[40:47])
gamma = float(header[47:54])
alpha *= np.pi / 180.0
beta *= np.pi / 180.0
gamma *= np.pi / 180.0
h = mt.abc2h(a, b, c, alpha, beta, gamma)
cell = Cell(h)
natoms = 0
body = filedesc.readline()
qatoms = []
names = []
masses = []
while (body.strip() != "" and body.strip() != "END"):
natoms += 1
name = body[12:16].strip()
names.append(name)
masses.append(Elements.mass(name))
x = float(body[31:39])
y = float(body[39:47])
z = float(body[47:55])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
body = filedesc.readline()
atoms = Atoms(natoms)
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names, dtype='|S4')
atoms.m = np.asarray(masses)
return atoms, cell
def read_pdb(filedesc):
"""Takes a pdb-style file and creates an Atoms and Cell object.
Args:
filedesc: An open readable file object from a pdb formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions,
and a Cell object with the appropriate cell dimensions and an estimate
of a reasonable cell mass.
"""
header = filedesc.readline()
if "TITLE" in header: header = filedesc.readline() # skip the comment field
if header == "":
raise EOFError("End of file or empty header in PDB file")
a = float(header[6:15])
b = float(header[15:24])
c = float(header[24:33])
alpha = float(header[33:40])
beta = float(header[40:47])
gamma = float(header[47:54])
alpha *= np.pi/180.0
beta *= np.pi/180.0
gamma *= np.pi/180.0
h = mt.abc2h(a, b, c, alpha, beta, gamma)
cell = Cell(h)
natoms = 0
body = filedesc.readline()
qatoms = []
names = []
masses = []
while (body.strip() != "" and body.strip() != "END"):
natoms += 1
name = body[12:16].strip()
names.append(name)
masses.append(Elements.mass(name))
x = float(body[31:39])
y = float(body[39:47])
z = float(body[47:55])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
body = filedesc.readline()
atoms = Atoms(natoms)
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names,dtype='|S4')
atoms.m = np.asarray(masses)
return atoms, cell
def read_xyz(filedesc):
"""Takes a xyz-style file and creates an Atoms object.
Args:
filedesc: An open readable file object from a xyz formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions.
"""
natoms = filedesc.readline()
if natoms == "":
raise EOFError("The file descriptor hit EOF.")
natoms = int(natoms)
comment = filedesc.readline()
qatoms = []
names = []
masses = []
iat = 0
while (iat < natoms):
body = filedesc.readline()
if body.strip() == "":
break
body = body.split()
name = body[0]
names.append(name)
masses.append(Elements.mass(name))
x = float(body[1])
y = float(body[2])
z = float(body[3])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
iat += 1
if natoms != len(names):
raise ValueError(
"The number of atom records does not match the header of the xyz file."
)
atoms = Atoms(natoms)
# for i in range(natoms):
# nat = atoms[i]
# nat.q = qatoms[i]
# nat.name = names[i]
# nat.m = Elements.mass(names[i])
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names, dtype='|S4')
atoms.m = np.asarray(masses)
return atoms
def read_xyz(filedesc):
"""Takes a xyz-style file and creates an Atoms object.
Args:
filedesc: An open readable file object from a xyz formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions.
"""
natoms = filedesc.readline()
if natoms == "":
raise EOFError("The file descriptor hit EOF.")
natoms = int(natoms)
comment = filedesc.readline()
qatoms = []
names = []
masses = []
iat = 0
while iat < natoms:
body = filedesc.readline()
if body.strip() == "":
break
body = body.split()
name = body[0]
names.append(name)
masses.append(Elements.mass(name))
x = float(body[1])
y = float(body[2])
z = float(body[3])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
iat += 1
if natoms != len(names):
raise ValueError("The number of atom records does not match the header of the xyz file.")
atoms = Atoms(natoms)
# for i in range(natoms):
# nat = atoms[i]
# nat.q = qatoms[i]
# nat.name = names[i]
# nat.m = Elements.mass(names[i])
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names, dtype="|S4")
atoms.m = np.asarray(masses)
return atoms
