class VelocityVerlet_QMMM(MolecularDynamics):
"""
VelocityVerlet_QMMM(self, mol_qm, mol_mm, pot_qm, pot_mm, pot_qmmm, dt, nstep, \
restart, check_mdstop_dispersion, tlim)
** This is performing QM/MM MD-Simulation.
The necessary arguments are alomost same with the above.
However, when you put the molecule and potential instance, you must separate
QM and MM parts. And, you must add the pot_qmmm instnace, which handles the QM/MM
interface.
"""
def __init__(self, mol, mol_mm, pot, pot_mm, pot_qmmm, 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)
self.mol_mm = mol_mm
self.pot_mm = pot_mm
self.pot_qmmm = pot_qmmm
#print "position-3"
#print self.mol_mm.get_positions()
#print self.pot_mm.get_check_pbc
if self.pot_mm.get_check_pbc():
self.mol_mm.set_positions(self.pot_mm.get_pbc_adjusted(self.mol_mm.get_positions()))
self.count = 0
self.nrange = self.pot.get_nrange()
self.setup_output()
#print "position-2"
#print self.mol_mm.get_positions()
def run(self):
self.pot.calc(); self.pot_mm.calc(); self.pot_qmmm.calc()
#print "position-1"
#print self.mol_mm.get_positions()
#this is for logging at initial point
self.woutp.logging(self)
# loop for MD
while self.count < self.step:
self.count += 1
self.step()
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.pot.remove_outputs()
self.woutp.finalize(self)
def setup_output(self):
self.woutp = WriteOutputMD_QMMM()
self.woutp.start(self)
if self.restart: self.woutp.restart(self)
def step(self):
#print "position0"
#print self.mol_mm.get_positions()
dt = self.dt
get_accelerations_save = self.mol.get_accelerations()
self.mol.set_positions(self.mol.get_positions() + \
self.mol.get_velocities() * dt + 0.5 * \
get_accelerations_save * dt * dt)
get_accelerations_save_mm = self.mol_mm.get_accelerations()
#print "position1"
#print self.mol_mm.get_positions()
positions_mm = self.mol_mm.get_positions() + \
self.mol_mm.get_velocities() * dt + 0.5 * \
get_accelerations_save_mm * dt * dt
#print "position2"
#print self.mol_mm.get_positions()
if self.pot_mm.get_check_pbc():
self.mol_mm.set_positions(self.pot_mm.get_pbc_adjusted(positions_mm))
else: self.mol_mm.set_positions(positions_mm)
self.pot.calc(); self.pot_mm.calc(); self.pot_qmmm.calc()
self.mol.set_velocities(self.mol.get_velocities() + \
0.5 * (self.mol.get_accelerations() + \
get_accelerations_save) * dt)
self.mol_mm.set_velocities(self.mol_mm.get_velocities() + \
0.5 * (self.mol_mm.get_accelerations() + \
get_accelerations_save_mm) * dt)
self.elaptime += dt
class VelocityVerlet_QMMM(MolecularDynamics):
"""
VelocityVerlet_QMMM(self, mol_qm, mol_mm, pot_qm, pot_mm, pot_qmmm, dt, nstep, \
restart, check_mdstop_dispersion, tlim)
** This is performing QM/MM MD-Simulation.
The necessary arguments are alomost same with the above.
However, when you put the molecule and potential instance, you must separate
QM and MM parts. And, you must add the pot_qmmm instnace, which handles the QM/MM
interface.
"""
def __init__(self, mol, mol_mm, pot, pot_mm, pot_qmmm, 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)
self.mol_mm = mol_mm
self.pot_mm = pot_mm
self.pot_qmmm = pot_qmmm
#print "position-3"
#print self.mol_mm.get_positions()
#print self.pot_mm.get_check_pbc
if self.pot_mm.get_check_pbc():
self.mol_mm.set_positions(
self.pot_mm.get_pbc_adjusted(self.mol_mm.get_positions()))
self.count = 0
self.nrange = self.pot.get_nrange()
self.setup_output()
#print "position-2"
#print self.mol_mm.get_positions()
def run(self):
self.pot.calc()
self.pot_mm.calc()
self.pot_qmmm.calc()
#print "position-1"
#print self.mol_mm.get_positions()
#this is for logging at initial point
self.woutp.logging(self)
# loop for MD
while self.count < self.step:
self.count += 1
self.step()
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.pot.remove_outputs()
self.woutp.finalize(self)
def setup_output(self):
self.woutp = WriteOutputMD_QMMM()
self.woutp.start(self)
if self.restart: self.woutp.restart(self)
def step(self):
#print "position0"
#print self.mol_mm.get_positions()
dt = self.dt
get_accelerations_save = self.mol.get_accelerations()
self.mol.set_positions(self.mol.get_positions() + \
self.mol.get_velocities() * dt + 0.5 * \
get_accelerations_save * dt * dt)
get_accelerations_save_mm = self.mol_mm.get_accelerations()
#print "position1"
#print self.mol_mm.get_positions()
positions_mm = self.mol_mm.get_positions() + \
self.mol_mm.get_velocities() * dt + 0.5 * \
get_accelerations_save_mm * dt * dt
#print "position2"
#print self.mol_mm.get_positions()
if self.pot_mm.get_check_pbc():
self.mol_mm.set_positions(
self.pot_mm.get_pbc_adjusted(positions_mm))
else:
self.mol_mm.set_positions(positions_mm)
self.pot.calc()
self.pot_mm.calc()
self.pot_qmmm.calc()
self.mol.set_velocities(self.mol.get_velocities() + \
0.5 * (self.mol.get_accelerations() + \
get_accelerations_save) * dt)
self.mol_mm.set_velocities(self.mol_mm.get_velocities() + \
0.5 * (self.mol_mm.get_accelerations() + \
get_accelerations_save_mm) * dt)
self.elaptime += dt
def setup_output(self):
self.woutp = WriteOutputMD_QMMM()
self.woutp.start(self)
if self.restart: self.woutp.restart(self)
def setup_output(self):
self.woutp = WriteOutputMD_QMMM()
self.woutp.start(self)
if self.restart: self.woutp.restart(self)
