class VelocityVerlet(MolecularDynamics):
"""
VelocityVerlet(self, mol, pot, deltat, nstep, restart, check_mdstop_dispersion, tlim)
** This is performing QM or MM MD-Simulation.
mol => Molecular instance. Refer to the Molecule.py
pot => Potential instance. Refer to the Potential.py
deltat => time step
nstep => step number
restart => whether md starts in the middle. default is False
if restart is True, the initial condition is loaded from the restart file
and the output files are written continuously.
check_mdstop_dispersion => when atoms are widely dispersed, md is terminated.
default is False
tlim => set the time when md is finished.
default is inf. Usually, the run of md is controlled by nstep.
"""
def __init__(self, mol, pot, dt, nstep, restart=False, check_mdstop_dispersion = False,\
limit_dispersion = 20.0, tlim = float('inf')):
MolecularDynamics.__init__(self, mol, pot, dt, nstep, restart, check_mdstop_dispersion, limit_dispersion, tlim)
if self.pot.get_check_pbc: self.mol.set_positions(self.pot.get_pbc_adjusted(self.mol.get_positions()))
self.count = 0
self.nrange = self.pot.get_nrange()
self.setup_output()
def setup_output(self):
self.woutp = WriteOutputMD()
self.woutp.start(self)
if self.restart: self.woutp.restart(self)
def run(self):
#this is the potential energy caluculation at the initial point
self.pot.calc()
#this is for logging at the initial point
self.woutp.logging(self)
# loop for MD
for _ in xrange(self.nstep):
self.step()
self.count += 1
self.woutp.logging(self)
self.mdstop_time_trans()
if self.mdstop_time_trans(): break
if self.check_mdstop_dispersion and self.mdstop_atom_dispersion(): break
self.woutp.finalize(self)
def step(self):
accelerations_save = self.mol.get_accelerations()
positions = self.mol.get_positions() + \
self.mol.get_velocities() * self.dt + 0.5 * \
accelerations_save * self.dt * self.dt
if self.pot.get_check_pbc(): self.mol.set_positions(self.pot.get_pbc_adjusted(positions))
else: self.mol.set_positions(positions)
self.pot.calc()
self.mol.set_velocities(self.mol.get_velocities() + \
0.5 * (self.mol.get_accelerations() + \
accelerations_save) * self.dt)
self.elaptime += self.dt
def setup_output(self):
self.woutp = WriteOutputMD()
self.woutp.start(self)
if self.restart: self.woutp.restart(self)
def setup_output(self):
self.woutp = WriteOutputMD()
self.woutp.start(self)
if self.restart: self.woutp.restart(self)
class VelocityVerlet(MolecularDynamics):
"""
VelocityVerlet(self, mol, pot, deltat, nstep, restart, check_mdstop_dispersion, tlim)
** This is performing QM or MM MD-Simulation.
mol => Molecular instance. Refer to the Molecule.py
pot => Potential instance. Refer to the Potential.py
deltat => time step
nstep => step number
restart => whether md starts in the middle. default is False
if restart is True, the initial condition is loaded from the restart file
and the output files are written continuously.
check_mdstop_dispersion => when atoms are widely dispersed, md is terminated.
default is False
tlim => set the time when md is finished.
default is inf. Usually, the run of md is controlled by nstep.
"""
def __init__(self, mol, pot, dt, nstep, restart=False, check_mdstop_dispersion = False,\
limit_dispersion = 20.0, tlim = float('inf')):
MolecularDynamics.__init__(self, mol, pot, dt, nstep, restart,
check_mdstop_dispersion, limit_dispersion,
tlim)
if self.pot.get_check_pbc:
self.mol.set_positions(
self.pot.get_pbc_adjusted(self.mol.get_positions()))
self.count = 0
self.nrange = self.pot.get_nrange()
self.setup_output()
def setup_output(self):
self.woutp = WriteOutputMD()
self.woutp.start(self)
if self.restart: self.woutp.restart(self)
def run(self):
#this is the potential energy caluculation at the initial point
self.pot.calc()
#this is for logging at the initial point
self.woutp.logging(self)
# loop for MD
for _ in xrange(self.nstep):
self.step()
self.count += 1
self.woutp.logging(self)
self.mdstop_time_trans()
if self.mdstop_time_trans(): break
if self.check_mdstop_dispersion and self.mdstop_atom_dispersion():
break
self.woutp.finalize(self)
def step(self):
accelerations_save = self.mol.get_accelerations()
positions = self.mol.get_positions() + \
self.mol.get_velocities() * self.dt + 0.5 * \
accelerations_save * self.dt * self.dt
if self.pot.get_check_pbc():
self.mol.set_positions(self.pot.get_pbc_adjusted(positions))
else:
self.mol.set_positions(positions)
self.pot.calc()
self.mol.set_velocities(self.mol.get_velocities() + \
0.5 * (self.mol.get_accelerations() + \
accelerations_save) * self.dt)
self.elaptime += self.dt