class TullySurfaceHopping_QMMM_Rigid(TullySurfaceHopping):
def __init__(self, mol_qm, mol_mm, pot_qm, pot_mm, pot_qmmm, dt, nstep, tsh_times, restart = False, \
tsh_ediff_thresh=0.05, tsh_ediff_factor=0.25, check_mdstop_dispersion = False, limit_dispersion = 10.0, \
tlim = float('inf')):
self.mol_mm = mol_mm
self.pot_mm = pot_mm
self.pot_qmmm = pot_qmmm
TullySurfaceHopping.__init__(self,mol_qm ,pot_qm, dt, nstep, tsh_times, restart,\
tsh_ediff_thresh, tsh_ediff_factor, check_mdstop_dispersion, limit_dispersion, tlim)
def setup_output(self):
self.woutp = WriteOutputMD_TSH_QMMM()
if self.restart: self.woutp.restart(self)
else: self.woutp.start(self)
def prepare(self):
self.pot.calc(); self.pot_mm.calc(); self.pot_qmmm.calc()
self.pre_judge_tsh()
self.check_ediff()
def step(self):
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)
self.pot.calc(); self.pot_qmmm.calc()
self.mol.set_velocities(self.mol.get_velocities() + \
0.5 * (self.mol.get_accelerations() + \
get_accelerations_save) * dt)
self.elaptime += dt
class TullySurfaceHopping_QMMM(TullySurfaceHopping):
def __init__(self, mol_qm, mol_mm, pot_qm, pot_mm, pot_qmmm, dt, nstep, tsh_times= 10, restart = False, \
tsh_ediff_thresh=0.05, tsh_ediff_factor=0.25, check_mdstop_dispersion = False, \
limit_dispersion = 10.0, tlim = float('inf')):
self.mol_mm = mol_mm
self.pot_mm = pot_mm
self.pot_qmmm = pot_qmmm
if self.pot_mm.get_check_pbc:
self.mol_mm.set_positions(
self.pot_mm.get_pbc_adjusted(self.mol_mm.get_positions()))
TullySurfaceHopping.__init__(self,mol_qm ,pot_qm, dt, nstep, tsh_times, restart,\
tsh_ediff_thresh, tsh_ediff_factor, check_mdstop_dispersion, limit_dispersion, tlim)
def setup_output(self):
self.woutp = WriteOutputMD_TSH_QMMM()
if self.restart: self.woutp.restart(self)
else: self.woutp.start(self)
def prepare(self):
#self.pot.calc(self.count); self.pot_mm.calc(); self.pot_qmmm.calc()
self.pot.calc()
self.pot_mm.calc()
self.pot_qmmm.calc()
self.pre_judge_tsh()
self.check_ediff()
def step(self):
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()
self.mol_mm.set_positions(self.mol_mm.get_positions() + \
self.mol_mm.get_velocities() * dt + 0.5 * \
get_accelerations_save_mm * dt * dt)
if self.pot_mm.get_check_pbc:
self.mol_mm.set_positions(
self.pot_mm.get_pbc_adjusted(self.mol_mm.get_positions()))
#self.pot.calc(self.count); self.pot_mm.calc(); self.pot_qmmm.calc()
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 TullySurfaceHopping_QMMM(TullySurfaceHopping):
def __init__(self, mol_qm, mol_mm, pot_qm, pot_mm, pot_qmmm, dt, nstep, tsh_times= 10, restart = False, \
tsh_ediff_thresh=0.02, tsh_ediff_factor=0.2, check_mdstop_dispersion = False, \
limit_dispersion = 10.0, tlim = float('inf'), change_cas_condition = False):
self.mol_mm = mol_mm
self.pot_mm = pot_mm
self.pot_qmmm = pot_qmmm
if self.pot_mm.get_check_pbc:
self.mol_mm.set_positions(self.pot_mm.get_pbc_adjusted(self.mol_mm.get_positions()))
TullySurfaceHopping.__init__(self,mol_qm ,pot_qm, dt, nstep, tsh_times, restart,\
tsh_ediff_thresh, tsh_ediff_factor, check_mdstop_dispersion, limit_dispersion, tlim, change_cas_condition)
def setup_output(self):
self.woutp = WriteOutputMD_TSH_QMMM()
if self.restart: self.woutp.restart(self)
else: self.woutp.start(self)
def prepare(self):
#self.pot.calc(self.count); self.pot_mm.calc(); self.pot_qmmm.calc()
self.pot.calc(); self.pot_mm.calc(); self.pot_qmmm.calc()
self.pre_judge_tsh()
self.check_ediff()
def step(self):
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()
self.mol_mm.set_positions(self.mol_mm.get_positions() + \
self.mol_mm.get_velocities() * dt + 0.5 * \
get_accelerations_save_mm * dt * dt)
if self.pot_mm.get_check_pbc:
self.mol_mm.set_positions(self.pot_mm.get_pbc_adjusted(self.mol_mm.get_positions()))
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_TSH_QMMM()
if self.restart: self.woutp.restart(self)
else: self.woutp.start(self)
def setup_output(self):
self.woutp = WriteOutputMD_TSH_QMMM()
if self.restart: self.woutp.restart(self)
else: self.woutp.start(self)
