def __init__(self, atoms, timestep, trajectory, logfile=None,
loginterval=1, append_trajectory=False):
# dt as to be attached _before_ parent class is initialized
self.dt = timestep
Dynamics.__init__(self, atoms, logfile=None, trajectory=trajectory,
append_trajectory=append_trajectory)
self.masses = self.atoms.get_masses()
self.max_steps = None
if 0 in self.masses:
warnings.warn('Zero mass encountered in atoms; this will '
'likely lead to errors if the massless atoms '
'are unconstrained.')
self.masses.shape = (-1, 1)
if not self.atoms.has('momenta'):
self.atoms.set_momenta(np.zeros([len(self.atoms), 3]))
if logfile:
self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile),
interval=loginterval)
def __init__(self,
atoms,
timestep,
integrator='verlet',
trajectory=None,
traj_interval=1000,
logfile=None,
loginterval=100):
Dynamics.__init__(self, atoms, None, None)
self.dt = timestep
if integrator == 'verlet':
self.run_style = 'verlet'
else:
raise RuntimeError('Unknown integrator: %s' % thermostat)
if trajectory:
if isinstance(trajectory, str):
trajectory = PickleTrajectory(trajectory, 'w', atoms)
self.attach(trajectory, interval=traj_interval)
if logfile:
self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile),
interval=loginterval)
self.fix = None
self.cell_relaxed = False
def __init__(self,
atoms,
timestep,
trajectory,
logfile=None,
loginterval=1):
Dynamics.__init__(self, atoms, logfile=None, trajectory=trajectory)
self.dt = timestep
self.masses = self.atoms.get_masses()
self.masses.shape = (-1, 1)
if logfile:
self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile),
interval=loginterval)
def __init__(self, atoms, timestep, trajectory, logfile=None,
loginterval=1):
Dynamics.__init__(self, atoms, logfile=None, trajectory=trajectory)
self.dt = timestep
self.masses = self.atoms.get_masses()
if 0 in self.masses:
warnings.warn('Zero mass encountered in atoms; this will '
'likely lead to errors if the massless atoms '
'are unconstrained.')
self.masses.shape = (-1, 1)
if logfile:
self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile),
interval=loginterval)
def md_run(origin_poscar_path, index):
print('%d' % index + ' In directory : %s' % origin_poscar_path)
atoms = read(origin_poscar_path)
calc = ANNCalculator(potentials={
"Ga": "Ga.10t-10t.nn",
"N": "N.10t-10t.nn"
})
atoms.set_calculator(calc)
MaxwellBoltzmannDistribution(atoms, 1200 * kB)
Stationary(atoms)
md = NVT(atoms, timestep=2 * fs, temperature=1000 * kB, friction=0.05)
logger = MDLogger(md, atoms, '-', stress=True)
md.attach(logger, interval=1)
traj = Trajectory(
"nvt_%s.traj" % (origin_poscar_path.split('/')[-1].split('.xsf')[0]),
"w", atoms)
md.attach(traj.write, interval=200)
md.run(40000)
def __init__(self,
atoms,
timestep,
trajectory,
logfile=None,
loginterval=1,
append_trajectory=False):
# dt as to be attached _before_ parent class is initialized
self.dt = timestep
Dynamics.__init__(self, atoms, logfile=None, trajectory=None)
self.masses = self.atoms.get_masses()
self.max_steps = None
if 0 in self.masses:
warnings.warn('Zero mass encountered in atoms; this will '
'likely lead to errors if the massless atoms '
'are unconstrained.')
self.masses.shape = (-1, 1)
if not self.atoms.has('momenta'):
self.atoms.set_momenta(np.zeros([len(self.atoms), 3]))
# Trajectory is attached here instead of in Dynamics.__init__
# to respect the loginterval argument.
if trajectory is not None:
if isinstance(trajectory, str):
mode = "a" if append_trajectory else "w"
trajectory = Trajectory(trajectory, mode=mode, atoms=atoms)
self.attach(trajectory, interval=loginterval)
if logfile:
self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile),
interval=loginterval)
def __init__(self, atoms, timestep, trajectory, logfile=None,
loginterval=1, append_trajectory=False):
"""Molecular Dynamics object.
Parameters:
atoms: Atoms object
The Atoms object to operate on.
timestep: float
The time step in ASE time units.
trajectory: Trajectory object or str
Attach trajectory object. If *trajectory* is a string a
Trajectory will be constructed. Use *None* for no
trajectory.
logfile: file object or str (optional)
If *logfile* is a string, a file with that name will be opened.
Use '-' for stdout.
loginterval: int (optional)
Only write a log line for every *loginterval* time steps.
Default: 1
append_trajectory: boolean (optional)
Defaults to False, which causes the trajectory file to be
overwriten each time the dynamics is restarted from scratch.
If True, the new structures are appended to the trajectory
file instead.
"""
# dt as to be attached _before_ parent class is initialized
self.dt = timestep
Dynamics.__init__(self, atoms, logfile=None, trajectory=None)
self.masses = self.atoms.get_masses()
self.max_steps = None
if 0 in self.masses:
warnings.warn('Zero mass encountered in atoms; this will '
'likely lead to errors if the massless atoms '
'are unconstrained.')
self.masses.shape = (-1, 1)
if not self.atoms.has('momenta'):
self.atoms.set_momenta(np.zeros([len(self.atoms), 3]))
# Trajectory is attached here instead of in Dynamics.__init__
# to respect the loginterval argument.
try:
if trajectory is not None:
if isinstance(trajectory, str):
mode = "a" if append_trajectory else "w"
trajectory = self.ensureclose(
Trajectory(trajectory, mode=mode, atoms=atoms)
)
self.attach(trajectory, interval=loginterval)
if logfile:
logger = self.ensureclose(
MDLogger(dyn=self, atoms=atoms, logfile=logfile))
self.attach(logger, loginterval)
except BaseException:
self._closefiles()
raise