def __init__(self, filename, mode='r', atoms=None,
backup=True, split=None, iolimit=10):
if split is None:
# Decide if subtype should be split based on number of atoms
split = (atoms is not None) and atoms.get_number_of_atoms() > 1000000
# Never use subtype split for serial simulations
if not getattr(atoms, "parallel", False):
split = False
# Use the collector object to join all data on master if subtype is normal
# and the simulation is parallel.
if not split and atoms is not None and getattr(atoms, "parallel", False):
atoms = asap3.Collector(atoms)
if split:
self.subtype = 'split'
else:
self.subtype = 'normal'
# self.iolimit may be needed if reading a split bundle.
if world.size < 1.5 * iolimit:
self.iolimit = None
else:
self.iolimit = iolimit
_BundleTrajectory.__init__(self, filename, mode, atoms,
backup=backup)
if self.subtype == 'split':
self.set_extra_data('ID') # So the atoms can be sorted when read.
def close(self):
"""Clean up when closing."""
if self.state == 'write' and self.master:
i = self.nframes
while True:
fname = os.path.join(self.filename, "F" + str(i))
if not os.path.exists(fname):
break
self.log("Closing, removing empty directory "+fname)
os.rmdir(fname)
i += 1
_BundleTrajectory.close(self)
def read_from_trajectory(cls, trajectory, frame=-1, atoms=None):
"""Read dynamics and atoms from trajectory (Class method).
Simultaneously reads the atoms and the dynamics from a BundleTrajectory,
including the internal data of the NPT dynamics object (automatically
saved when attaching a BundleTrajectory to an NPT object).
Arguments:
trajectory
The filename or an open BundleTrajectory object.
frame (optional)
Which frame to read. Default: the last.
atoms (optional, internal use only)
Pre-read atoms. Do not use.
"""
if isinstance(trajectory, str):
if trajectory.endswith("/"):
trajectory = trajectory[:-1]
if trajectory.endswith(".bundle"):
from ase.io.bundletrajectory import BundleTrajectory
trajectory = BundleTrajectory(trajectory)
else:
raise ValueError("Cannot open '%': unsupported file format" % trajectory)
# trajectory is now a BundleTrajectory object (or compatible)
if atoms is None:
atoms = trajectory[frame]
init_data = trajectory.read_extra_data("npt_init", 0)
frame_data = trajectory.read_extra_data("npt_dynamics", frame)
dyn = cls(
atoms,
timestep=init_data["dt"],
temperature=init_data["temperature"],
externalstress=init_data["externalstress"],
ttime=init_data["ttime"],
pfactor=init_data["pfactor_given"],
mask=init_data["mask"],
)
dyn.desiredEkin = init_data["desiredEkin"]
dyn.tfact = init_data["tfact"]
dyn.pfact = init_data["pfact"]
dyn.frac_traceless = init_data["frac_traceless"]
for k, v in frame_data.items():
setattr(dyn, k, v)
return (dyn, atoms)
def read_from_trajectory(cls, trajectory, frame=-1, atoms=None):
"""Read dynamics and atoms from trajectory (Class method).
Simultaneously reads the atoms and the dynamics from a BundleTrajectory,
including the internal data of the NPT dynamics object (automatically
saved when attaching a BundleTrajectory to an NPT object).
Arguments:
trajectory
The filename or an open BundleTrajectory object.
frame (optional)
Which frame to read. Default: the last.
atoms (optional, internal use only)
Pre-read atoms. Do not use.
"""
if isinstance(trajectory, str):
if trajectory.endswith('/'):
trajectory = trajectory[:-1]
if trajectory.endswith('.bundle'):
from ase.io.bundletrajectory import BundleTrajectory
trajectory = BundleTrajectory(trajectory)
else:
raise ValueError("Cannot open '%': unsupported file format" %
trajectory)
# trajectory is now a BundleTrajectory object (or compatible)
if atoms is None:
atoms = trajectory[frame]
init_data = trajectory.read_extra_data('npt_init', 0)
frame_data = trajectory.read_extra_data('npt_dynamics', frame)
dyn = cls(atoms,
timestep=init_data['dt'],
temperature=init_data['temperature'],
externalstress=init_data['externalstress'],
ttime=init_data['ttime'],
pfactor=init_data['pfactor_given'],
mask=init_data['mask'])
dyn.desiredEkin = init_data['desiredEkin']
dyn.tfact = init_data['tfact']
dyn.pfact = init_data['pfact']
dyn.frac_traceless = init_data['frac_traceless']
for k, v in frame_data.items():
setattr(dyn, k, v)
return (dyn, atoms)
def test_append_bundle(images, bundletraj):
traj = BundleTrajectory(bundletraj, mode='a')
assert len(read(bundletraj, ':')) == 2
#write(bundletraj, images, append=True)
for atoms in images:
traj.write(atoms)
traj.close()
images1 = read(bundletraj, ':')
assert len(images1) == 4
# XXX Fix the magmoms/charges bug
assert_images_equal(images * 2, images1)
def filetype(filename):
"""Try to guess the type of the file."""
if os.path.isdir(filename):
# Potentially a BundleTrajectory
if BundleTrajectory.is_bundle(filename):
return 'bundle'
elif os.path.normpath(filename) == 'states':
return 'eon'
else:
raise IOError('Directory: ' + filename)
if filename.startswith('pg://'):
return 'postgresql'
fileobj = open(filename, 'rU')
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if s3.startswith('{"'):
return 'json'
if filename.endswith('.db'):
return 'db'
if filename.lower().endswith('.cmr'):
return 'cmr'
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
if hasattr(nc, 'file_format') and nc.file_format.startswith('ETSF'):
return 'etsf'
raise IOError('Unknown netCDF file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith('PickleTrajectory'):
return 'traj'
if (lines[1].startswith('OUTER LOOP:')
or filename.lower().endswith('.cube')):
return 'cube'
if ' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for line in lines:
if line[0] != '#':
word = line.strip()
if word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
return 'xsf'
filename_v = os.path.basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if 'OUTCAR' in filename_v:
return 'vasp_out'
if filename.lower().endswith('.exi'):
return 'exi'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if filename.lower().endswith('.struct'):
return 'struct'
if filename.lower().endswith('.struct_out'):
return 'struct_out'
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if 'Invoking FHI-aims ...' in line:
return 'aims_out'
if 'atom' in line:
data = line.split()
try:
Atoms(symbols=[data[4]],
positions=[[
float(data[1]),
float(data[2]),
float(data[3])
]])
return 'aims'
except:
pass
if filename.lower().endswith('.in'):
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if ('&system' in line) or ('&SYSTEM' in line):
return 'esp_in'
return 'aims'
if filename.lower().endswith('.cfg'):
return 'cfg'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
if lines[0].startswith('$coord') or os.path.basename(filename) == 'coord':
return 'tmol'
if (lines[0].startswith('$grad')
or os.path.basename(filename) == 'gradient'):
return 'tmol-gradient'
if lines[0].startswith('Geometry'):
return 'dftb'
if filename.lower().endswith('.geom'):
return 'castep_geom'
if filename.lower().endswith('.castep'):
return 'castep'
if filename.lower().endswith('.cell'):
return 'castep_cell'
if s3 == '<?x':
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if filename.lower().endswith('.sdf'):
return 'sdf'
if filename.lower().endswith('.gen'):
return 'gen'
if filename.lower().endswith('.con'):
return 'eon'
if 'ITEM: TIMESTEP\n' in lines:
return 'lammps'
if filename.lower().endswith('.gro'):
return 'gromacs'
if filename.lower().endswith('.log'):
return 'gaussian_out'
if filename.lower().endswith('.com'):
return 'gaussian'
if filename.lower().endswith('.g96'):
return 'gromos'
if filename.lower().endswith('.out'):
return 'esp_out'
if filename.endswith('.nw'):
return 'nw'
return 'xyz'
def filetype(filename):
"""Try to guess the type of the file."""
if os.path.isdir(filename):
# Potentially a BundleTrajectory
if BundleTrajectory.is_bundle(filename):
return 'bundle'
elif os.path.normpath(filename) == 'states':
return 'eon'
else:
raise IOError('Directory: ' + filename)
if filename.startswith('pg://'):
return 'postgresql'
fileobj = open(filename, 'rb')
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if s3.startswith(b'{"'):
return 'json'
if filename.endswith('.db'):
return 'db'
if filename.lower().endswith('.cmr'):
return 'cmr'
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
if hasattr(nc, 'file_format') and nc.file_format.startswith('ETSF'):
return 'etsf'
raise IOError('Unknown netCDF file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith(b'AFFormatASE-Trajectory'):
return 'traj'
if lines[0].startswith(b'PickleTrajectory'):
return 'trj'
if (lines[1].startswith(b'OUTER LOOP:') or
filename.lower().endswith('.cube')):
return 'cube'
if b' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (b' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for line in lines:
if line[0] != b'#':
word = line.strip()
if word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
return 'xsf'
filename_v = os.path.basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if 'OUTCAR' in filename_v:
return 'vasp_out'
if 'XDATCAR' in filename_v:
return 'vasp_xdatcar'
if filename.lower().endswith('.exi'):
return 'exi'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if filename.lower().endswith('.struct'):
return 'struct'
if filename.lower().endswith('.struct_out'):
return 'struct_out'
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if b'Invoking FHI-aims ...' in line:
return 'aims_out'
if b'atom' in line:
data = line.split()
try:
Atoms(symbols=[data[4]],
positions=[[float(data[1]),
float(data[2]),
float(data[3])]])
return 'aims'
except:
pass
if filename.lower().endswith('.in'):
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if ('&system' in line) or ('&SYSTEM' in line):
return 'esp_in'
return 'aims'
if filename.lower().endswith('.cfg'):
return 'cfg'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
if lines[0].startswith(b'$coord') or os.path.basename(filename) == 'coord':
return 'tmol'
if (lines[0].startswith(b'$grad') or
os.path.basename(filename) == 'gradient'):
return 'tmol-gradient'
if lines[0].startswith(b'Geometry'):
return 'dftb'
if filename.lower().endswith('.geom'):
return 'castep_geom'
if filename.lower().endswith('.castep'):
return 'castep'
if filename.lower().endswith('.cell'):
return 'castep_cell'
if s3 == '<?x' and not filename.endswith('xsd'):
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if filename.lower().endswith('.sdf'):
return 'sdf'
if filename.lower().endswith('.gen'):
return 'gen'
if filename.lower().endswith('.con'):
return 'eon'
if 'ITEM: TIMESTEP\n' in lines:
return 'lammps'
if filename.lower().endswith('.gro'):
return 'gromacs'
if filename.lower().endswith('.log'):
return 'gaussian_out'
if filename.lower().endswith('.com'):
return 'gaussian'
if filename.lower().endswith('.g96'):
return 'gromos'
if filename.lower().endswith('.out'):
return 'esp_out'
if filename.endswith('.nw'):
return 'nw'
if filename.endswith('xsd'):
return 'xsd'
return 'xyz'
def filetype(filename):
"""Try to guess the type of the file."""
if os.path.isdir(filename):
# Potentially a BundleTrajectory
if BundleTrajectory.is_bundle(filename):
return 'bundle'
else:
raise IOError('Directory: ' + filename)
fileobj = open(filename)
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
if hasattr(nc, 'file_format') and nc.file_format.startswith('ETSF'):
return 'etsf'
raise IOError('Unknown netCDF file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith('PickleTrajectory'):
return 'traj'
if lines[1].startswith('OUTER LOOP:') or filename.lower().endswith(
'.cube'):
return 'cube'
if ' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for line in lines:
if line[0] != '#':
word = line.strip()
if word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
return 'xsf'
filename_v = basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if 'OUTCAR' in filename_v:
return 'vasp_out'
if filename.lower().endswith('.exi'):
return 'exi'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if filename.lower().endswith('.struct'):
return 'struct'
if filename.lower().endswith('.in'):
return 'aims'
if filename.lower().endswith('.out'):
return 'aims_out'
if filename.lower().endswith('.cfg'):
return 'cfg'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
if lines[0].startswith('$coord'):
return 'tmol'
if lines[0].startswith('Geometry'):
return 'dftb'
if s3 == '<?x':
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if filename.lower().endswith('.sdf'):
return 'sdf'
return 'xyz'
def _set_defaults(self):
subtype = self.subtype # Preserve it
_BundleTrajectory._set_defaults(self)
self.subtype = subtype
self.datatypes['forces'] = False
def write(self, atoms=None):
if self.subtype == 'normal' and atoms is not None and getattr(atoms, "parallel", False):
atoms = asap3.Collector(atoms)
_BundleTrajectory.write(self, atoms)