def __init__(self, f, units, sub=slice(None)):
"""
Arguments:
| ``f`` -- a filename or a file-like object
| ``units`` -- The units of the atom fields. The number of fields,
their unit and their meaning depends on the input
file of the LAMMPS simulation.
Optional argumtent:
| ``sub`` -- a slice object indicating which time frames to skip/read
"""
SlicedReader.__init__(self, f, sub)
# first read the number of atoms
try:
while True:
line = next(self._f)
if line == "ITEM: NUMBER OF ATOMS\n":
break
try:
line = next(self._f)
self.num_atoms = int(line)
except ValueError:
raise FileFormatError("Could not read the number of atoms. Expected an integer. Got '%s'" % line)
except StopIteration:
raise FileFormatError("Could not find line 'ITEM: NUMBER OF ATOMS'.")
self._f.seek(0) # go back to the beginning of the file
self.units = units
def __init__(self, f, sub=slice(None), pos_unit=angstrom,
vel_unit=angstrom/picosecond, frc_unit=amu*angstrom/picosecond**2,
time_unit=picosecond, mass_unit=amu
):
"""
Arguments:
| ``f`` -- a filename or a file-like object
Optional arguments:
| ``sub`` -- a slice indicating the frames to be skipped/selected
| ``pos_unit``, ``vel_unit``, ``frc_unit``, ``time_unit``,
``mass_unit`` -- The conversion factors for the unit conversion
from the units in the data file to atomic units. The defaults of
these optional arguments correspond to the defaults of dlpoly.
"""
SlicedReader.__init__(self, f, sub)
self._counter = 1 # make our counter compatible with dlpoly
self.pos_unit = pos_unit
self.vel_unit = vel_unit
self.frc_unit = frc_unit
self.time_unit = time_unit
self.mass_unit = mass_unit
try:
self.header = self._f.next()[:-1]
integers = tuple(int(word) for word in self._f.next().split())
if len(integers) != 3:
raise FileFormatError("Second line must contain three integers.")
self.keytrj, self.imcon, self.num_atoms = integers
except StopIteration:
raise FileFormatError("File is too short. Could not read header.")
except ValueError:
raise FileFormatError("Second line must contain three integers.")
self._frame_size = 4 + self.num_atoms*(self.keytrj+2)
def __init__(self, f, units, sub=slice(None)):
"""
Arguments:
| ``f`` -- a filename or a file-like object
| ``units`` -- The units of the atom fields. The number of fields,
their unit and their meaning depends on the input
file of the LAMMPS simulation.
Optional argumtent:
| ``sub`` -- a slice object indicating which time frames to skip/read
"""
SlicedReader.__init__(self, f, sub)
# first read the number of atoms
try:
while True:
line = self._f.next()
if line == "ITEM: NUMBER OF ATOMS\n":
break
try:
line = self._f.next()
self.num_atoms = int(line)
except ValueError:
raise FileFormatError("Could not read the number of atoms. Expected an integer. Got '%s'" % line)
except StopIteration:
raise FileFormatError("Could not find line 'ITEM: NUMBER OF ATOMS'.")
self._f.seek(0) # go back to the beginning of the file
self.units = units
def __init__(
self,
f,
sub=slice(None),
pos_unit=angstrom,
vel_unit=angstrom / picosecond,
frc_unit=amu * angstrom / picosecond**2,
time_unit=picosecond,
mass_unit=amu,
restart=False,
):
"""
Arguments:
| ``f`` -- a filename or a file-like object
Optional arguments:
| ``sub`` -- a slice indicating the frames to be skipped/selected
| ``pos_unit``, ``vel_unit``, ``frc_unit``, ``time_unit``,
``mass_unit`` -- The conversion factors for the unit conversion
from the units in the data file to atomic units. The defaults of
these optional arguments correspond to the defaults of dlpoly.
When the file starts with a line that satisfies the following
conditions, it is assumed that this is a history restart file:
* line consists of 6 words
* first word equals 'timestep'
* the following for words are integers
* the last word is a float
"""
SlicedReader.__init__(self, f, sub)
self._counter = 1 # make our counter compatible with dlpoly
self.pos_unit = pos_unit
self.vel_unit = vel_unit
self.frc_unit = frc_unit
self.time_unit = time_unit
self.mass_unit = mass_unit
restart = self._detect_restart()
if restart is None:
try:
self.header = next(self._f)[:-1]
integers = tuple(int(word) for word in next(self._f).split())
if len(integers) != 3:
raise FileFormatError(
"Second line must contain three integers.")
self.keytrj, self.imcon, self.num_atoms = integers
except StopIteration:
raise FileFormatError(
"File is too short. Could not read header.")
except ValueError:
raise FileFormatError(
"Second line must contain three integers.")
else:
self.header = ''
self.num_atoms, self.keytrj, self.imcon = restart
self._frame_size = 4 + self.num_atoms * (self.keytrj + 2)
def __init__(self, f, sub=slice(None)):
"""
Argument:
| ``f`` -- a filename or a file-like object
Optional argument:
| ``sub`` -- a slice object to indicate the frames to be read/skipped.
"""
SlicedReader.__init__(self, f, sub)
self.num_atoms = None
pos = self._read_frame()[1]
self.num_atoms = len(pos)
self._f.seek(0)
def __init__(self, f, sub=slice(None)):
"""
Argument:
| ``f`` -- a filename or a file-like object
Optional argument:
| ``sub`` -- a slice object to indicate the frames to be read/skipped.
"""
SlicedReader.__init__(self, f, sub)
self.num_atoms = None
pos = self._read_frame()[1]
self.num_atoms = len(pos)
self._f.seek(0)
def __init__(self, f, sub=slice(None)):
"""
Arguments:
| ``f`` -- a filename or a file-like object
| ``sub`` -- an optional slice object to select a subset of time
frames
The number of atoms is read immediately and is available as
``self.num_atoms``.
"""
SlicedReader.__init__(self, f, sub)
self._secfile = SectionFile(self._f)
self._read_header()
def __init__(self, f, sub=slice(None)):
"""
Arguments:
| ``f`` -- a filename or a file-like object
| ``sub`` -- an optional slice object to select a subset of time
frames
The number of atoms is read immediately and is available as
``self.num_atoms``.
"""
SlicedReader.__init__(self, f, sub)
self._secfile = SectionFile(self._f)
self._read_header()
def __init__(self, f, sub=slice(None), pos_unit=angstrom,
vel_unit=angstrom/picosecond, frc_unit=amu*angstrom/picosecond**2,
time_unit=picosecond, mass_unit=amu, restart=False,
):
"""
Arguments:
| ``f`` -- a filename or a file-like object
Optional arguments:
| ``sub`` -- a slice indicating the frames to be skipped/selected
| ``pos_unit``, ``vel_unit``, ``frc_unit``, ``time_unit``,
``mass_unit`` -- The conversion factors for the unit conversion
from the units in the data file to atomic units. The defaults of
these optional arguments correspond to the defaults of dlpoly.
When the file starts with a line that satisfies the following
conditions, it is assumed that this is a history restart file:
* line consists of 6 words
* first word equals 'timestep'
* the following for words are integers
* the last word is a float
"""
SlicedReader.__init__(self, f, sub)
self._counter = 1 # make our counter compatible with dlpoly
self.pos_unit = pos_unit
self.vel_unit = vel_unit
self.frc_unit = frc_unit
self.time_unit = time_unit
self.mass_unit = mass_unit
restart = self._detect_restart()
if restart is None:
try:
self.header = self._f.next()[:-1]
integers = tuple(int(word) for word in self._f.next().split())
if len(integers) != 3:
raise FileFormatError("Second line must contain three integers.")
self.keytrj, self.imcon, self.num_atoms = integers
except StopIteration:
raise FileFormatError("File is too short. Could not read header.")
except ValueError:
raise FileFormatError("Second line must contain three integers.")
else:
self.header = ''
self.num_atoms, self.keytrj, self.imcon = restart
self._frame_size = 4 + self.num_atoms*(self.keytrj+2)
def __init__(self, f, sub=slice(None)):
"""
Arguments:
| ``f`` -- a filename or a file-like object
Optional argument:
| ``sub`` -- a slice object indicating which time frames to skip/read
"""
SlicedReader.__init__(self, f, sub)
# first determine the number of atoms
s = None
self.num_atoms = 0
for line in self._f:
if s is None:
s = line[:7]
elif s != line[:7]:
break
self.num_atoms += 1
self._f.seek(0) # go back to the beginning of the file
def __init__(self, f, sub=slice(None)):
"""
Arguments:
| ``f`` -- a filename or a file-like object
Optional argument:
| ``sub`` -- a slice object indicating which time frames to skip/read
"""
SlicedReader.__init__(self, f, sub)
# first determine the number of atoms
s = None
self.num_atoms = 0
for line in self._f:
if s is None:
s = line[:7]
elif s != line[:7]:
break
self.num_atoms += 1
self._f.seek(0) # go back to the beginning of the file
def __init__(self, f, sub=slice(None), file_unit=angstrom):
"""Initialize an XYZ reader
Arguments:
| ``f`` -- a filename or a file-like object
Optional arguments:
| ``sub`` -- a slice indicating which frames to read/skip
| ``file_unit`` -- the conversion constant to convert data into atomic
units [default=angstrom]
After initialization, the following attributes are defined:
| ``symbols`` -- The atom symbols
| ``numbers`` -- The atom numbers
"""
SlicedReader.__init__(self, f, sub)
self.file_unit = file_unit
try:
self.symbols = None
self._first = self._read_frame()
self.numbers = numpy.zeros(len(self.symbols), int)
for index, symbol in enumerate(self.symbols):
try:
number = int(symbol)
symbol = periodic[number].symbol
self.symbols[index] = symbol
except ValueError:
atom_info = periodic[symbol]
if atom_info is not None:
number = atom_info.number
else:
number = 0
self.numbers[index] = number
self.symbols = tuple(self.symbols)
self._f.seek(0)
except StopIteration:
raise FileFormatError(
"Could not read first frame from XYZ file. Incorrect file format."
)
def __init__(self, f, sub=slice(None), skip_equi_period=True,
pos_unit=angstrom, time_unit=picosecond, angle_unit=deg,
e_unit=amu/(angstrom/picosecond)**2
):
"""
Arguments:
| ``f`` -- a filename or a file-like object
Optional arguments:
| ``sub`` -- a slice indicating the frames to be skipped/selected
| ``skip_equi_period`` -- When True, the equilibration period is
not read [default=True]
| ``pos_unit``, ``time_unit``, ``angle_unit``, ``e_unit`` -- The
conversion factors for the unit conversion from the units in the
data file to atomic units. The defaults of these optional
arguments correspond to the defaults of dlpoly.
"""
SlicedReader.__init__(self, f, sub)
self._counter = 1 # make our counter compatible with dlpoly
self.skip_equi_period = skip_equi_period
self._conv = [
1, e_unit, 1, e_unit, e_unit, e_unit, e_unit, e_unit, e_unit, e_unit,
time_unit, e_unit, 1, e_unit, e_unit, e_unit, e_unit, e_unit, e_unit, e_unit,
1, pos_unit**3, 1, e_unit, e_unit, angle_unit, angle_unit, angle_unit, e_unit, 1000*atm,
]
# find the line that gives the number of equilibration steps:
try:
while True:
line = self._f.next()
if line.startswith(" equilibration period"):
self.equi_period = int(line[30:])
break
except StopIteration:
raise FileFormatError("DL_POLY OUTPUT file is too short. Could not find line with the number of equilibration steps.")
except ValueError:
raise FileFormatError("Could not read the number of equilibration steps. (expecting an integer)")
def __init__(self, f, sub=slice(None), skip_equi_period=True,
pos_unit=angstrom, time_unit=picosecond, angle_unit=deg,
e_unit=amu/(angstrom/picosecond)**2
):
"""
Arguments:
| ``f`` -- a filename or a file-like object
Optional arguments:
| ``sub`` -- a slice indicating the frames to be skipped/selected
| ``skip_equi_period`` -- When True, the equilibration period is
not read [default=True]
| ``pos_unit``, ``time_unit``, ``angle_unit``, ``e_unit`` -- The
conversion factors for the unit conversion from the units in the
data file to atomic units. The defaults of these optional
arguments correspond to the defaults of dlpoly.
"""
SlicedReader.__init__(self, f, sub)
self._counter = 1 # make our counter compatible with dlpoly
self.skip_equi_period = skip_equi_period
self._conv = [
1, e_unit, 1, e_unit, e_unit, e_unit, e_unit, e_unit, e_unit, e_unit,
time_unit, e_unit, 1, e_unit, e_unit, e_unit, e_unit, e_unit, e_unit, e_unit,
1, pos_unit**3, 1, e_unit, e_unit, angle_unit, angle_unit, angle_unit, e_unit, 1000*atm,
]
# find the line that gives the number of equilibration steps:
try:
while True:
line = next(self._f)
if line.startswith(" equilibration period"):
self.equi_period = int(line[30:])
break
except StopIteration:
raise FileFormatError("DL_POLY OUTPUT file is too short. Could not find line with the number of equilibration steps.")
except ValueError:
raise FileFormatError("Could not read the number of equilibration steps. (expecting an integer)")
def __init__(self, f, sub=slice(None), file_unit=angstrom):
"""Initialize an XYZ reader
Arguments:
| ``f`` -- a filename or a file-like object
Optional arguments:
| ``sub`` -- a slice indicating which frames to read/skip
| ``file_unit`` -- the conversion constant to convert data into atomic
units [default=angstrom]
After initialization, the following attributes are defined:
| ``symbols`` -- The atom symbols
| ``numbers`` -- The atom numbers
"""
SlicedReader.__init__(self, f, sub)
self.file_unit = file_unit
try:
self.symbols = None
self._first = self._read_frame()
self.numbers = numpy.zeros(len(self.symbols), int)
for index, symbol in enumerate(self.symbols):
try:
number = int(symbol)
symbol = periodic[number].symbol
self.symbols[index] = symbol
except ValueError:
atom_info = periodic[symbol]
if atom_info is not None:
number = atom_info.number
else:
number = 0
self.numbers[index] = number
self.symbols = tuple(self.symbols)
self._f.seek(0)
except StopIteration:
raise FileFormatError("Could not read first frame from XYZ file. Incorrect file format.")
