def __init__(self, temp, start=0, step=1, select=None, annealing=1.0):
"""
This is an implementation of the Andersen thermostat. The method
is described in:
Andersen, H. C. J. Chem. Phys. 1980, 72, 2384-2393.
**Arguments:**
temp
The average temperature of the NVT ensemble
**Optional arguments:**
start
The first iteration at which this hook is called
step
The number of iterations between two subsequent calls to this
hook.
select
An array of atom indexes to indicate which atoms controlled by
the thermostat.
annealing
After every call to this hook, the temperature is multiplied
with this annealing factor. This effectively cools down the
system.
"""
self.temp = temp
self.select = select
self.annealing = annealing
VerletHook.__init__(self, start, step)
def __init__(self, temp, start=0, step=1, select=None, annealing=1.0):
"""
This is an implementation of the Andersen thermostat. The method
is described in:
Andersen, H. C. J. Chem. Phys. 1980, 72, 2384-2393.
**Arguments:**
temp
The average temperature of the NVT ensemble
**Optional arguments:**
start
The first iteration at which this hook is called
step
The number of iterations between two subsequent calls to this
hook.
select
An array of atom indexes to indicate which atoms controlled by
the thermostat.
annealing
After every call to this hook, the temperature is multiplied
with this annealing factor. This effectively cools down the
system.
"""
self.temp = temp
self.select = select
self.annealing = annealing
VerletHook.__init__(self, start, step)
def __init__(self, temp, press, start=0, step=1, amp=1e-3):
"""
Warning: this code is not fully tested yet!
**Arguments:**
temp
The average temperature of the NpT ensemble
press
The external pressure of the NpT ensemble
**Optional arguments:**
start
The first iteration at which this hook is called
step
The number of iterations between two subsequent calls to this
hook.
amp
The amplitude of the changes in the logarithm of the volume.
"""
self.temp = temp
self.press = press
self.amp = amp
self.dim = 3
self.baro_ndof = 1
VerletHook.__init__(self, start, step)
def __init__(self, temp, press, start=0, step=1, amp=1e-3):
"""
Warning: this code is not fully tested yet!
**Arguments:**
temp
The average temperature of the NpT ensemble
press
The external pressure of the NpT ensemble
**Optional arguments:**
start
The first iteration at which this hook is called
step
The number of iterations between two subsequent calls to this
hook.
amp
The amplitude of the changes in the logarithm of the volume.
"""
self.temp = temp
self.press = press
self.amp = amp
self.dim = 3
self.baro_ndof = 1
VerletHook.__init__(self, start, step)
def __init__(self, temp, start=0, timecon=100*femtosecond, restart=False):
"""
This is an implementation of the Berendsen thermostat. The algorithm
is described in:
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.;
Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Berendsen thermostat.
restart
Indicates whether the initalisation should be carried out.
"""
self.temp = temp
self.timecon = timecon
self.restart = restart
VerletHook.__init__(self, start, 1)
def __init__(self, temp, a_p, c_p=None, start=0):
"""
This hook implements the coloured noise thermostat. The equations
are derived in:
Ceriotti, M.; Bussi, G.; Parrinello, M J. Chem. Theory Comput.
2010, 6, 1170-1180.
**Arguments:**
temp
The temperature of thermostat.
a_p
Square drift matrix, with elements fitted to the specific problem.
**Optional arguments:**
c_p
Square static covariance matrix. In equilibrium, its elements are fixed.
For non-equilibrium dynamics, its elements should be fitted.
start
The step at which the thermostat becomes active.
"""
self.temp = temp
self.ns = int(a_p.shape[0] - 1)
self.a_p = a_p
self.c_p = c_p
if self.c_p is None:
# Assume equilibrium dynamics if c_p is not provided
self.c_p = boltzmann * self.temp * np.eye(self.ns + 1)
VerletHook.__init__(self, start, 1)
def __init__(self, thermostat, barostat, start=0):
"""
VerletHook combining an arbitrary Thermostat and Barostat instance, which
ensures these instances are called in the correct succession, and possible
coupling between both is handled correctly.
**Arguments:**
thermostat
A Thermostat instance
barostat
A Barostat instance
"""
self.thermostat = thermostat
self.barostat = barostat
self.start = start
# verify if thermostat and barostat instances are currently supported in yaff
if not self.verify():
self.barostat = thermostat
self.thermostat = barostat
if not self.verify():
raise TypeError('The Thermostat or Barostat instance is not supported (yet)')
self.step_thermo = self.thermostat.step
self.step_baro = self.barostat.step
VerletHook.__init__(self, start, min(self.step_thermo, self.step_baro))
def __init__(self, temp, start=0, timecon=100*femtosecond):
"""
This is an implementation of the CSVR thermostat. The equations are
derived in:
Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007,
126, 014101
The implementation (used here) is derived in
Bussi, G.; Parrinello, M. Comput. Phys. Commun. 2008, 179, 26-29
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the CSVR thermostat.
"""
self.temp = temp
self.timecon = timecon
VerletHook.__init__(self, start, 1)
def __init__(self, temp, start=0, timecon=100 * femtosecond):
"""
This is an implementation of the CSVR thermostat. The equations are
derived in:
Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007,
126, 014101
The implementation (used here) is derived in
Bussi, G.; Parrinello, M. Comput. Phys. Commun. 2008, 179, 26-29
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the CSVR thermostat.
"""
self.temp = temp
self.timecon = timecon
VerletHook.__init__(self, start, 1)
def __init__(self,
temp,
start=0,
timecon=100 * femtosecond,
restart=False):
"""
This is an implementation of the Berendsen thermostat. The algorithm
is described in:
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.;
Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Berendsen thermostat.
restart
Indicates whether the initalisation should be carried out.
"""
self.temp = temp
self.timecon = timecon
self.restart = restart
VerletHook.__init__(self, start, 1)
def __init__(self, temp, start=0, timecon=100*femtosecond, chainlength=3):
"""
This hook implements the Nose-Hoover-Chain thermostat. The equations
are derived in:
Martyna, G. J.; Klein, M. L.; Tuckerman, M. J. Chem. Phys. 1992,
97, 2635-2643.
The implementation (used here) of a symplectic integrator of the
Nose-Hoover-Chain thermostat is discussed in:
Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein,
M. L. Mol. Phys. 1996, 87, 1117-1157.
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Nose-Hoover thermostat.
chainlength
The number of beads in the Nose-Hoover chain.
"""
self.temp = temp
# At this point, the timestep and the number of degrees of freedom are
# not known yet.
self.chain = NHChain(chainlength, 0.0, temp, 0, timecon)
VerletHook.__init__(self, start, 1)
def __init__(self, temp, a_p, c_p=None, start=0):
"""
This hook implements the coloured noise thermostat. The equations
are derived in:
Ceriotti, M.; Bussi, G.; Parrinello, M J. Chem. Theory Comput.
2010, 6, 1170-1180.
**Arguments:**
temp
The temperature of thermostat.
a_p
Square drift matrix, with elements fitted to the specific problem.
**Optional arguments:**
c_p
Square static covariance matrix. In equilibrium, its elements are fixed.
For non-equilibrium dynamics, its elements should be fitted.
start
The step at which the thermostat becomes active.
"""
self.temp = temp
self.ns = int(a_p.shape[0]-1)
self.a_p = a_p
self.c_p = c_p
if self.c_p is None:
# Assume equilibrium dynamics if c_p is not provided
self.c_p = boltzmann*self.temp*np.eye(self.ns+1)
VerletHook.__init__(self, start, 1)
def __init__(self, thermostat, barostat, start=0):
"""
VerletHook combining an arbitrary Thermostat and Barostat instance, which
ensures these instances are called in the correct succession, and possible
coupling between both is handled correctly.
**Arguments:**
thermostat
A Thermostat instance
barostat
A Barostat instance
"""
self.thermostat = thermostat
self.barostat = barostat
self.start = start
# verify if thermostat and barostat instances are currently supported in yaff
if not self.verify():
self.barostat = thermostat
self.thermostat = barostat
if not self.verify():
raise TypeError('The Thermostat or Barostat instance is not supported (yet)')
self.step_thermo = self.thermostat.step
self.step_baro = self.barostat.step
VerletHook.__init__(self, start, min(self.step_thermo, self.step_baro))
def __init__(self,
temp,
start=0,
timecon=100 * femtosecond,
chainlength=3,
chain_pos0=None,
chain_vel0=None,
restart=False):
"""
This hook implements the Nose-Hoover chain thermostat. The equations
are derived in:
Martyna, G. J.; Klein, M. L.; Tuckerman, M. J. Chem. Phys. 1992,
97, 2635-2643.
The implementation (used here) of a symplectic integrator of the
Nose-Hoover chain thermostat is discussed in:
Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein,
M. L. Mol. Phys. 1996, 87, 1117-1157.
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Nose-Hoover thermostat.
chainlength
The number of beads in the Nose-Hoover chain.
chain_pos0
The initial thermostat chain positions
chain_vel0
The initial thermostat chain velocities
restart
Indicates whether the initalisation should be carried out
"""
self.temp = temp
self.restart = restart
# At this point, the timestep and the number of degrees of freedom are
# not known yet
self.chain = NHChain(chainlength, 0.0, temp, 0, chain_pos0, chain_vel0,
timecon)
VerletHook.__init__(self, start, 1)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, beta=4.57e-5/bar, anisotropic=True, vol_constraint=False, restart=False):
"""
This hook implements the Berendsen barostat. The equations are derived in:
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.;
Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied pressure for the barostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Berendsen barostat.
beta
The isothermal compressibility, conventionally the compressibility of liquid water
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
"""
self.temp = temp
self.press = press
self.timecon_press = timecon
self.beta = beta
self.mass_press = 3.0*timecon/beta
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.dim = ff.system.cell.nvec
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic:
# symmetrize the cell tensor
cell_symmetrize(ff)
self.cell = ff.system.cell.rvecs.copy()
self.restart = restart
VerletHook.__init__(self, start, step)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, beta=4.57e-5/bar, anisotropic=True, vol_constraint=False, restart=False):
"""
This hook implements the Berendsen barostat. The equations are derived in:
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.;
Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied pressure for the barostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Berendsen barostat.
beta
The isothermal compressibility, conventionally the compressibility of liquid water
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
"""
self.temp = temp
self.press = press
self.timecon_press = timecon
self.beta = beta
self.mass_press = 3.0*timecon/beta
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.dim = ff.system.cell.nvec
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic:
# symmetrize the cell tensor
cell_symmetrize(ff)
self.cell = ff.system.cell.rvecs.copy()
self.restart = restart
VerletHook.__init__(self, start, step)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, anisotropic=True, vol_constraint=False):
"""
This hook implements the Langevin barostat. The equations are derived in:
Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R.
J. Chem. Phys. 1995, 103, 4613-4621
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied pressure for the barostat.
**Optional arguments:**
start
The step at which the barostat becomes active.
timecon
The time constant of the Langevin barostat.
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
"""
self.temp = temp
self.press = press
self.timecon = timecon
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.dim = ff.system.cell.nvec
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic:
# symmetrize the cell tensor
cell_symmetrize(ff)
self.cell = ff.system.cell.rvecs.copy()
VerletHook.__init__(self, start, step)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, anisotropic=True, vol_constraint=False):
"""
This hook implements the Langevin barostat. The equations are derived in:
Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R.
J. Chem. Phys. 1995, 103, 4613-4621
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied pressure for the barostat.
**Optional arguments:**
start
The step at which the barostat becomes active.
timecon
The time constant of the Langevin barostat.
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
"""
self.temp = temp
self.press = press
self.timecon = timecon
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.dim = ff.system.cell.nvec
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic:
# symmetrize the cell tensor
cell_symmetrize(ff)
self.cell = ff.system.cell.rvecs.copy()
VerletHook.__init__(self, start, step)
def __init__(self, temp, start=0, timecon=100*femtosecond, chainlength=3, chain_pos0=None, chain_vel0=None, restart=False):
"""
This hook implements the Nose-Hoover chain thermostat. The equations
are derived in:
Martyna, G. J.; Klein, M. L.; Tuckerman, M. J. Chem. Phys. 1992,
97, 2635-2643.
The implementation (used here) of a symplectic integrator of the
Nose-Hoover chain thermostat is discussed in:
Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein,
M. L. Mol. Phys. 1996, 87, 1117-1157.
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Nose-Hoover thermostat.
chainlength
The number of beads in the Nose-Hoover chain.
chain_pos0
The initial thermostat chain positions
chain_vel0
The initial thermostat chain velocities
restart
Indicates whether the initalisation should be carried out
"""
self.temp = temp
self.restart = restart
# At this point, the timestep and the number of degrees of freedom are
# not known yet
self.chain = NHChain(chainlength, 0.0, temp, 0, chain_pos0, chain_vel0, timecon)
VerletHook.__init__(self, start, 1)
def __init__(self, temp, start=0, timecon=100 * femtosecond):
"""
This is an implementation of the Langevin thermostat. The algorithm
is described in:
Bussi, G.; Parrinello, M. Phys. Rev. E 2007, 75, 056707
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Langevin thermostat.
"""
self.temp = temp
self.timecon = timecon
VerletHook.__init__(self, start, 1)
def __init__(self, temp, start=0, timecon=100*femtosecond):
"""
This is an implementation of the Langevin thermostat. The algorithm
is described in:
Bussi, G.; Parrinello, M. Phys. Rev. E 2007, 75, 056707
**Arguments:**
temp
The temperature of thermostat.
**Optional arguments:**
start
The step at which the thermostat becomes active.
timecon
The time constant of the Langevin thermostat.
"""
self.temp = temp
self.timecon = timecon
VerletHook.__init__(self, start, 1)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, anisotropic=True, vol_constraint=False, baro_thermo=None, vel_press0=None, restart=False):
"""
This hook implements the Martyna-Tobias-Klein barostat. The equations
are derived in:
Martyna, G. J.; Tobias, D. J.; Klein, M. L. J. Chem. Phys. 1994,
101, 4177-4189.
The implementation (used here) of a symplectic integrator of this
barostat is discussed in
Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein,
M. L. Mol. Phys. 1996, 87, 1117-1157.
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied pressure for the barostat.
**Optional arguments:**
start
The step at which the barostat becomes active.
timecon
The time constant of the Martyna-Tobias-Klein barostat.
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
baro_thermo
NHCThermostat instance, coupled directly to the barostat
vel_press0
The initial barostat velocity tensor
restart
If true, the cell is not symmetrized initially
"""
self.temp = temp
self.press = press
self.timecon_press = timecon
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.baro_thermo = baro_thermo
self.dim = ff.system.cell.nvec
self.restart = restart
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic and not self.restart:
# symmetrize the cell tensor
cell_symmetrize(ff)
self.cell = ff.system.cell.rvecs.copy()
self.vel_press = vel_press0
VerletHook.__init__(self, start, step)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, anisotropic=True, vol_constraint=False, baro_thermo=None, vel_press0=None, restart=False):
"""
This hook implements the Tadmor-Miller barostat for finite strains.
The equations are derived in:
Tadmor, E. B.; Miller, R. E. Modeling Materials: Continuum,
Atomistic and Multiscale Techniques 2011, 520-527.
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied second Piola-Kirchhoff tensor for the barostat.
**Optional arguments:**
start
The step at which the barostat becomes active.
timecon
The time constant of the Tadmor-Miller barostat.
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
baro_thermo
NHCThermostat instance, coupled directly to the barostat
vel_press0
The initial barostat velocity tensor
restart
If true, the cell is not symmetrized initially
"""
self.temp = temp
self.press = press
self.timecon_press = timecon
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.baro_thermo = baro_thermo
self.dim = ff.system.cell.nvec
self.restart = restart
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic and not self.restart:
# symmetrize the cell tensor
cell_symmetrize(ff)
self.cell = ff.system.cell.rvecs.copy()
self.cellinv0 = np.linalg.inv(self.cell)
self.vol0 = ff.system.cell.volume
# definition of h0^{-1} S h_0^{-T}
self.Strans = np.dot(np.dot(self.cellinv0, self.press), self.cellinv0.T)
self.vel_press = vel_press0
VerletHook.__init__(self, start, step)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, anisotropic=True, vol_constraint=False, baro_thermo=None, vel_press0=None, restart=False):
"""
This hook implements the Parrinello-Rahman barostat for finite strains.
The equations are derived in:
Parrinello, M.; Rahman, A. J. Appl. Phys. 1981, 52, 7182-7190.
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied pressure for the barostat.
**Optional arguments:**
start
The step at which the barostat becomes active.
timecon
The time constant of the Tadmor-Miller barostat.
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
baro_thermo
NHCThermostat instance, coupled directly to the barostat
vel_press0
The initial barostat velocity tensor
restart
If true, the cell is not symmetrized initially
"""
self.temp = temp
if isinstance(press, np.ndarray):
self.press = press
else:
self.press = press*np.eye(3)
self.timecon_press = timecon
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.baro_thermo = baro_thermo
self.dim = ff.system.cell.nvec
self.restart = restart
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic and not self.restart:
# symmetrize the cell and stress tensor
vc, tn = cell_symmetrize(ff, tensor_list=[self.press])
self.press = tn[0]
self.P = np.trace(self.press)/3
self.S_ani = self.press - self.P*np.eye(3)
self.S_ani = 0.5*(self.S_ani + self.S_ani.T) # only symmetric part of stress tensor contributes to individual motion
self.cellinv0 = np.linalg.inv(ff.system.cell.rvecs.copy())
self.vol0 = ff.system.cell.volume
# definition of Sigma = V_0*h_0^{-1} S_ani h_0^{-T}
self.Sigma = self.vol0*np.dot(np.dot(self.cellinv0.T, self.S_ani), self.cellinv0)
self.vel_press = vel_press0
VerletHook.__init__(self, start, step)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, anisotropic=True, vol_constraint=False, baro_thermo=None, vel_press0=None, restart=False):
"""
This hook implements the Tadmor-Miller barostat for finite strains.
The equations are derived in:
Tadmor, E. B.; Miller, R. E. Modeling Materials: Continuum,
Atomistic and Multiscale Techniques 2011, 520-527.
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied second Piola-Kirchhoff tensor for the barostat.
**Optional arguments:**
start
The step at which the barostat becomes active.
timecon
The time constant of the Tadmor-Miller barostat.
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
baro_thermo
NHCThermostat instance, coupled directly to the barostat
vel_press0
The initial barostat velocity tensor
restart
If true, the cell is not symmetrized initially
"""
self.temp = temp
self.press = press
self.timecon_press = timecon
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.baro_thermo = baro_thermo
self.dim = ff.system.cell.nvec
self.restart = restart
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic and not self.restart:
# symmetrize the cell tensor
cell_symmetrize(ff)
self.cell = ff.system.cell.rvecs.copy()
self.cellinv0 = np.linalg.inv(self.cell)
self.vol0 = ff.system.cell.volume
# definition of h0^{-1} S h_0^{-T}
self.Strans = np.dot(np.dot(self.cellinv0, self.press), self.cellinv0.T)
self.vel_press = vel_press0
VerletHook.__init__(self, start, step)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, anisotropic=True, vol_constraint=False, baro_thermo=None, vel_press0=None, restart=False):
"""
This hook implements the Parrinello-Rahman barostat for finite strains.
The equations are derived in:
Parrinello, M.; Rahman, A. J. Appl. Phys. 1981, 52, 7182-7190.
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied pressure for the barostat.
**Optional arguments:**
start
The step at which the barostat becomes active.
timecon
The time constant of the Tadmor-Miller barostat.
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
baro_thermo
NHCThermostat instance, coupled directly to the barostat
vel_press0
The initial barostat velocity tensor
restart
If true, the cell is not symmetrized initially
"""
self.temp = temp
if isinstance(press, np.ndarray):
self.press = press
else:
self.press = press*np.eye(3)
self.timecon_press = timecon
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.baro_thermo = baro_thermo
self.dim = ff.system.cell.nvec
self.restart = restart
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic and not self.restart:
# symmetrize the cell and stress tensor
vc, tn = cell_symmetrize(ff, tensor_list=[self.press])
self.press = tn[0]
self.P = np.trace(self.press)/3
self.S_ani = self.press - self.P*np.eye(3)
self.S_ani = 0.5*(self.S_ani + self.S_ani.T) # only symmetric part of stress tensor contributes to individual motion
self.cellinv0 = np.linalg.inv(ff.system.cell.rvecs.copy())
self.vol0 = ff.system.cell.volume
# definition of Sigma = V_0*h_0^{-1} S_ani h_0^{-T}
self.Sigma = self.vol0*np.dot(np.dot(self.cellinv0.T, self.S_ani), self.cellinv0)
self.vel_press = vel_press0
VerletHook.__init__(self, start, step)
def __init__(self, ff, temp, press, start=0, step=1, timecon=1000*femtosecond, anisotropic=True, vol_constraint=False, baro_thermo=None, vel_press0=None, restart=False):
"""
This hook implements the Martyna-Tobias-Klein barostat. The equations
are derived in:
Martyna, G. J.; Tobias, D. J.; Klein, M. L. J. Chem. Phys. 1994,
101, 4177-4189.
The implementation (used here) of a symplectic integrator of this
barostat is discussed in
Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein,
M. L. Mol. Phys. 1996, 87, 1117-1157.
**Arguments:**
ff
A ForceField instance.
temp
The temperature of thermostat.
press
The applied pressure for the barostat.
**Optional arguments:**
start
The step at which the barostat becomes active.
timecon
The time constant of the Martyna-Tobias-Klein barostat.
anisotropic
Defines whether anisotropic cell fluctuations are allowed.
vol_constraint
Defines whether the volume is allowed to fluctuate.
baro_thermo
NHCThermostat instance, coupled directly to the barostat
vel_press0
The initial barostat velocity tensor
restart
If true, the cell is not symmetrized initially
"""
self.temp = temp
self.press = press
self.timecon_press = timecon
self.anisotropic = anisotropic
self.vol_constraint = vol_constraint
self.baro_thermo = baro_thermo
self.dim = ff.system.cell.nvec
self.restart = restart
# determine the number of degrees of freedom associated with the unit cell
self.baro_ndof = get_ndof_baro(self.dim, self.anisotropic, self.vol_constraint)
if self.anisotropic and not self.restart:
# symmetrize the cell tensor
cell_symmetrize(ff)
self.cell = ff.system.cell.rvecs.copy()
self.vel_press = vel_press0
VerletHook.__init__(self, start, step)
