def __init__(self,
filename=None,
create_indices=True,
use_lock_file=False):
self.filename = filename
self.create_indices = create_indices
if use_lock_file and isinstance(filename, str):
self.lock = Lock(filename + '.lock', world=DummyMPI())
else:
self.lock = None
def __init__(self,
filename=None,
create_indices=True,
use_lock_file=False):
self.filename = filename
self.create_indices = create_indices
if use_lock_file:
self.lock = Lock(filename + '.lock', world=DummyMPI())
else:
self.lock = None
self.timestamp = None # timestamp form last write
def __init__(self, filename=None, create_indices=True,
use_lock_file=False, serial=False):
"""Database object.
serial: bool
Let someone else handle parallelization. Default behavior is
to interact with the database on the master only and then
distribute results to all slaves.
"""
if isinstance(filename, basestring):
filename = os.path.expanduser(filename)
self.filename = filename
self.create_indices = create_indices
if use_lock_file and isinstance(filename, basestring):
self.lock = Lock(filename + '.lock', world=DummyMPI())
else:
self.lock = None
self.serial = serial
self._metadata = None # decription of columns and other stuff
def rank():
import sys
# Check for special MPI-enabled Python interpreters:
if '_gpaw' in sys.builtin_module_names:
import _gpaw # http://wiki.fysik.dtu.dk/gpaw
world = _gpaw.Communicator()
elif '_asap' in sys.builtin_module_names:
import _asap # http://wiki.fysik.dtu.dk/asap, can't import asap3.mpi here (import deadlock)
world = _asap.Communicator()
elif 'asapparallel3' in sys.modules: # Older version of Asap
import asapparallel3
world = asapparallel3.Communicator()
elif 'Scientific_mpi' in sys.modules:
from Scientific.MPI import world
elif 'mpi4py' in sys.modules:
world = MPI4PY()
else:
from ase.parallel import DummyMPI
world = DummyMPI() # This is a standard Python interpreter:
rank = world.rank
size = world.size
return rank
om = 5
pz = Placzek(
H2,
KSSingles,
gsname=gsname,
exname=exname,
verbose=True,
)
ai = pz.absolute_intensity(omega=om)[-1]
equal(ai, 301.659994669, 1e-3) # earlier obtained value
i = pz.intensity(omega=om)[-1]
equal(i, 7.87430831452e-05, 1e-11) # earlier obtained value
pz.summary(omega=5, method='frederiksen')
# parallel ------------------------
if world.size > 1 and world.rank == 0:
# single core
comm = DummyMPI()
pzsi = Placzek(
H2,
KSSingles,
gsname=gsname,
exname=exname,
comm=comm,
verbose=True,
)
isi = pzsi.intensity(omega=om)[-1]
equal(isi, i, 1e-11)
def __init__(self,
atoms,
timestep,
temperature_K,
andersen_prob,
fixcm=True,
trajectory=None,
logfile=None,
loginterval=1,
communicator=world,
rng=random,
append_trajectory=False):
""""
Parameters:
atoms: Atoms object
The list of atoms.
timestep: float
The time step in ASE time units.
temperature_K: float
The desired temperature, in Kelvin.
andersen_prob: float
A random collision probability, typically 1e-4 to 1e-1.
With this probability atoms get assigned random velocity components.
fixcm: bool (optional)
If True, the position and momentum of the center of mass is
kept unperturbed. Default: True.
rng: RNG object (optional)
Random number generator, by default numpy.random. Must have a
random_sample method matching the signature of
numpy.random.random_sample.
logfile: file object or str (optional)
If *logfile* is a string, a file with that name will be opened.
Use '-' for stdout.
trajectory: Trajectory object or str (optional)
Attach trajectory object. If *trajectory* is a string a
Trajectory will be constructed. Use *None* (the default) for no
trajectory.
communicator: MPI communicator (optional)
Communicator used to distribute random numbers to all tasks.
Default: ase.parallel.world. Set to None to disable communication.
append_trajectory: bool (optional)
Defaults to False, which causes the trajectory file to be
overwritten each time the dynamics is restarted from scratch.
If True, the new structures are appended to the trajectory
file instead.
The temperature is imposed by stochastic collisions with a heat bath
that acts on velocity components of randomly chosen particles.
The algorithm randomly decorrelates velocities, so dynamical properties
like diffusion or viscosity cannot be properly measured.
H. C. Andersen, J. Chem. Phys. 72 (4), 2384–2393 (1980)
"""
self.temp = units.kB * temperature_K
self.andersen_prob = andersen_prob
self.fix_com = fixcm
self.rng = rng
if communicator is None:
communicator = DummyMPI()
self.communicator = communicator
MolecularDynamics.__init__(self,
atoms,
timestep,
trajectory,
logfile,
loginterval,
append_trajectory=append_trajectory)
def __init__(self, atoms, timestep, temperature=None, friction=None,
fixcm=True, *, temperature_K=None, trajectory=None,
logfile=None, loginterval=1, communicator=world,
rng=None, append_trajectory=False):
"""
Parameters:
atoms: Atoms object
The list of atoms.
timestep: float
The time step in ASE time units.
temperature: float (deprecated)
The desired temperature, in electron volt.
temperature_K: float
The desired temperature, in Kelvin.
friction: float
A friction coefficient, typically 1e-4 to 1e-2.
fixcm: bool (optional)
If True, the position and momentum of the center of mass is
kept unperturbed. Default: True.
rng: RNG object (optional)
Random number generator, by default numpy.random. Must have a
standard_normal method matching the signature of
numpy.random.standard_normal.
logfile: file object or str (optional)
If *logfile* is a string, a file with that name will be opened.
Use '-' for stdout.
trajectory: Trajectory object or str (optional)
Attach trajectory object. If *trajectory* is a string a
Trajectory will be constructed. Use *None* (the default) for no
trajectory.
communicator: MPI communicator (optional)
Communicator used to distribute random numbers to all tasks.
Default: ase.parallel.world. Set to None to disable communication.
append_trajectory: bool (optional)
Defaults to False, which causes the trajectory file to be
overwritten each time the dynamics is restarted from scratch.
If True, the new structures are appended to the trajectory
file instead.
The temperature and friction are normally scalars, but in principle one
quantity per atom could be specified by giving an array.
RATTLE constraints can be used with these propagators, see:
E. V.-Eijnden, and G. Ciccotti, Chem. Phys. Lett. 429, 310 (2006)
The propagator is Equation 23 (Eq. 39 if RATTLE constraints are used)
of the above reference. That reference also contains another
propagator in Eq. 21/34; but that propagator is not quasi-symplectic
and gives a systematic offset in the temperature at large time steps.
"""
if friction is None:
raise TypeError("Missing 'friction' argument.")
self.fr = friction
self.temp = units.kB * self._process_temperature(temperature,
temperature_K, 'eV')
self.fix_com = fixcm
if communicator is None:
communicator = DummyMPI()
self.communicator = communicator
if rng is None:
self.rng = np.random
else:
self.rng = rng
MolecularDynamics.__init__(self, atoms, timestep, trajectory,
logfile, loginterval,
append_trajectory=append_trajectory)
self.updatevars()
