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 __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 __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()
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()
def __init__(self, mol, pot, dt, nstep, tsh_times = 5, restart = False,\
tsh_ediff_thresh=0.1, tsh_ediff_factor=0.25, check_mdstop_dispersion = False,\
limit_dispersion = 10.0, tlim = float('inf')):
MolecularDynamics.__init__(self, mol, pot, dt, nstep, restart,\
check_mdstop_dispersion, limit_dispersion, tlim)
self.now_state = self.pot.get_now_state()
self.nrange = self.pot.get_nrange()
self.m_root = np.sqrt(self.mol.get_masses())
self.tsh_times = tsh_times
self.delta_st = 0.5 * self.dt / self.tsh_times
self.dt_bak = self.dt
self.tsh_ediff_thresh = tsh_ediff_thresh
self.tsh_ediff_factor = tsh_ediff_factor
self.c = np.zeros(self.nrange)
self.c[self.now_state] = 1.0
self.count = 0
self.count_tsh = 0
self.setup_output()
def __init__(self, mol, pot, dt, nstep, tsh_times = 5, restart = False,\
tsh_ediff_thresh=0.1, tsh_ediff_factor=0.25, check_mdstop_dispersion = False,\
limit_dispersion = 10.0, tlim = float('inf')):
MolecularDynamics.__init__(self, mol, pot, dt, nstep, restart,\
check_mdstop_dispersion, limit_dispersion, tlim)
self.now_state = self.pot.get_now_state()
self.nrange = self.pot.get_nrange()
self.m_root = np.sqrt(self.mol.get_masses())
self.tsh_times = tsh_times
self.delta_st = 0.5 * self.dt / self.tsh_times
self.dt_bak = self.dt
self.tsh_ediff_thresh = tsh_ediff_thresh
self.tsh_ediff_factor = tsh_ediff_factor
self.c = np.zeros(self.nrange)
self.c[self.now_state] = 1.0
self.count = 0
self.count_tsh = 0
self.setup_output()