def init(self, iterative):
self.timestep_press = iterative.timestep
if not self.restart:
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# determine the internal degrees of freedom
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(len(iterative.ff.system.numbers), iterative.ff.system.cell.nvec)
# determine barostat 'mass' following W = timecon*np.sqrt(n_part) * m_av
#n_part = len(iterative.masses)
#self.mass_press = self.timecon_press*np.sum(iterative.masses)/np.sqrt(len(iterative.ff.system.numbers))
angfreq = 2*np.pi/self.timecon_press
self.mass_press = (iterative.ndof+self.dim**2)*boltzmann*self.temp/angfreq**2/self.vol0**(2./3)
if self.vel_press is None:
# define initial barostat velocity
self.vel_press = get_random_vel_press(self.mass_press, self.temp)
if not self.anisotropic:
self.vel_press = self.vel_press[0][0]
# initialize the barostat thermostat if present
if self.baro_thermo is not None:
self.baro_thermo.chain.timestep = iterative.timestep
self.baro_thermo.chain.set_ndof(self.baro_ndof)
# make sure the volume of the cell will not change if applicable
if self.vol_constraint:
self.vel_press -= np.trace(self.vel_press)/3*np.eye(3)
# compute gpos and vtens, since they differ
# after symmetrising the cell tensor
iterative.gpos[:] = 0.0
iterative.vtens[:] = 0.0
iterative.epot = iterative.ff.compute(iterative.gpos,iterative.vtens)
def init(self, iterative):
self.timestep_press = iterative.timestep
if not self.restart:
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# determine the internal degrees of freedom
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(len(iterative.ff.system.numbers), iterative.ff.system.cell.nvec)
# determine barostat 'mass' following W = timecon*np.sqrt(n_part) * m_av
#n_part = len(iterative.masses)
#self.mass_press = self.timecon_press*np.sum(iterative.masses)/np.sqrt(len(iterative.ff.system.numbers))
angfreq = 2*np.pi/self.timecon_press
self.mass_press = (iterative.ndof+self.dim**2)*boltzmann*self.temp/angfreq**2/self.vol0**(2./3)
if self.vel_press is None:
# define initial barostat velocity
self.vel_press = get_random_vel_press(self.mass_press, self.temp)
if not self.anisotropic:
self.vel_press = self.vel_press[0][0]
# initialize the barostat thermostat if present
if self.baro_thermo is not None:
self.baro_thermo.chain.timestep = iterative.timestep
self.baro_thermo.chain.set_ndof(self.baro_ndof)
# make sure the volume of the cell will not change if applicable
if self.vol_constraint:
self.vel_press -= np.trace(self.vel_press)/3*np.eye(3)
# compute gpos and vtens, since they differ
# after symmetrising the cell tensor
iterative.gpos[:] = 0.0
iterative.vtens[:] = 0.0
iterative.epot = iterative.ff.compute(iterative.gpos,iterative.vtens)
def init(self, iterative):
# It is mandatory to zero the external momenta.
clean_momenta(iterative.pos, iterative.vel, iterative.masses,
iterative.ff.system.cell)
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(
iterative.pos.shape[0], iterative.ff.system.cell.nvec)
self.kin = 0.5 * iterative.ndof * boltzmann * self.temp
def init(self, iterative):
if not self.restart:
# It is mandatory to zero the external momenta.
clean_momenta(iterative.pos, iterative.vel, iterative.masses,
iterative.ff.system.cell)
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(
iterative.pos.shape[0], iterative.ff.system.cell.nvec)
def init(self, iterative):
# It is mandatory to zero the external momenta.
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# If needed, determine the number of _internal_ degrees of freedom.
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(iterative.pos.shape[0], iterative.ff.system.cell.nvec)
# Configure the chain.
self.chain.timestep = iterative.timestep
self.chain.set_ndof(iterative.ndof)
def init(self, iterative):
# It is mandatory to zero the external momenta
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# Initialize the additional momenta
self.s = 0.5*boltzmann*self.temp*np.random.normal(size=(self.ns, iterative.pos.size))
# Determine the update matrices
eigval, eigvec = np.linalg.eig(-self.a_p * iterative.timestep/2)
self.t = np.dot(eigvec*np.exp(eigval), np.linalg.inv(eigvec)).real
self.S = stabilized_cholesky_decomp(self.c_p - np.dot(np.dot(self.t,self.c_p),self.t.T)).real
# Store the number of atoms for later use
self.n_atoms = iterative.pos.shape[0]
def init(self, iterative):
if not self.restart:
# It is mandatory to zero the external momenta
clean_momenta(iterative.pos, iterative.vel, iterative.masses,
iterative.ff.system.cell)
# If needed, determine the number of _internal_ degrees of freedom
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(
iterative.pos.shape[0], iterative.ff.system.cell.nvec)
# Configure the chain
self.chain.timestep = iterative.timestep
self.chain.set_ndof(iterative.ndof)
def init(self, iterative):
self.timestep_press = iterative.timestep
if not self.restart:
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# compute gpos and vtens, since they differ
# after symmetrising the cell tensor
iterative.gpos[:] = 0.0
iterative.vtens[:] = 0.0
iterative.epot = iterative.ff.compute(iterative.gpos,iterative.vtens)
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(iterative.pos.shape[0], iterative.ff.system.cell.nvec)
# rescaling of the barostat mass, to be in accordance with Langevin and MTTK
self.mass_press *= np.sqrt(iterative.ndof)
def init(self, iterative):
self.timestep_press = iterative.timestep
if not self.restart:
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# compute gpos and vtens, since they differ
# after symmetrising the cell tensor
iterative.gpos[:] = 0.0
iterative.vtens[:] = 0.0
iterative.epot = iterative.ff.compute(iterative.gpos,iterative.vtens)
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(iterative.pos.shape[0], iterative.ff.system.cell.nvec)
# rescaling of the barostat mass, to be in accordance with Langevin and MTTK
self.mass_press *= np.sqrt(iterative.ndof)
def init(self, iterative):
# It is mandatory to zero the external momenta
clean_momenta(iterative.pos, iterative.vel, iterative.masses,
iterative.ff.system.cell)
# Initialize the additional momenta
self.s = 0.5 * boltzmann * self.temp * np.random.normal(
size=(self.ns, iterative.pos.size))
# Determine the update matrices
eigval, eigvec = np.linalg.eig(-self.a_p * iterative.timestep / 2)
self.t = np.dot(eigvec * np.exp(eigval), np.linalg.inv(eigvec)).real
self.S = stabilized_cholesky_decomp(
self.c_p - np.dot(np.dot(self.t, self.c_p), self.t.T)).real
# Store the number of atoms for later use
self.n_atoms = iterative.pos.shape[0]
def pre(self, iterative, G1_add = None):
# Andersen thermostat step before usual Verlet hook, since it largely affects the velocities
# Needed to correct the conserved quantity
ekin_before = iterative._compute_ekin()
# Change the (selected) velocities
if self.select is None:
iterative.vel[:] = get_random_vel(self.temp, False, iterative.masses)
else:
iterative.vel[self.select] = get_random_vel(self.temp, False, iterative.masses, self.select)
# Zero any external momenta after choosing new velocities
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# Update the kinetic energy and the reference for the conserved quantity
ekin_after = iterative._compute_ekin()
self.econs_correction += ekin_before - ekin_after
# Optional annealing
self.temp *= self.annealing
def pre(self, iterative, G1_add=None):
# Andersen thermostat step before usual Verlet hook, since it largely affects the velocities
# Needed to correct the conserved quantity
ekin_before = iterative._compute_ekin()
# Change the (selected) velocities
if self.select is None:
iterative.vel[:] = get_random_vel(self.temp, False,
iterative.masses)
else:
iterative.vel[self.select] = get_random_vel(
self.temp, False, iterative.masses, self.select)
# Zero any external momenta after choosing new velocities
clean_momenta(iterative.pos, iterative.vel, iterative.masses,
iterative.ff.system.cell)
# Update the kinetic energy and the reference for the conserved quantity
ekin_after = iterative._compute_ekin()
self.econs_correction += ekin_before - ekin_after
# Optional annealing
self.temp *= self.annealing
def init(self, iterative):
self.timestep_press = iterative.timestep
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# set the number of internal degrees of freedom (no restriction on p_cm)
if iterative.ndof is None:
iterative.ndof = iterative.pos.size
# define the barostat 'mass'
self.mass_press = (iterative.ndof+3)/3*boltzmann*self.temp*(self.timecon/(2*np.pi))**2
# define initial barostat velocity
self.vel_press = get_random_vel_press(self.mass_press, self.temp)
# make sure the volume of the cell will not change if applicable
if self.vol_constraint:
self.vel_press -= np.trace(self.vel_press)/3*np.eye(3)
if not self.anisotropic:
self.vel_press = self.vel_press[0][0]
# compute gpos and vtens, since they differ
# after symmetrising the cell tensor
iterative.gpos[:] = 0.0
iterative.vtens[:] = 0.0
iterative.epot = iterative.ff.compute(iterative.gpos,iterative.vtens)
def init(self, iterative):
self.timestep_press = iterative.timestep
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
# set the number of internal degrees of freedom (no restriction on p_cm)
if iterative.ndof is None:
iterative.ndof = iterative.pos.size
# define the barostat 'mass'
self.mass_press = (iterative.ndof+3)/3*boltzmann*self.temp*(self.timecon/(2*np.pi))**2
# define initial barostat velocity
self.vel_press = get_random_vel_press(self.mass_press, self.temp)
# make sure the volume of the cell will not change if applicable
if self.vol_constraint:
self.vel_press -= np.trace(self.vel_press)/3*np.eye(3)
if not self.anisotropic:
self.vel_press = self.vel_press[0][0]
# compute gpos and vtens, since they differ
# after symmetrising the cell tensor
iterative.gpos[:] = 0.0
iterative.vtens[:] = 0.0
iterative.epot = iterative.ff.compute(iterative.gpos,iterative.vtens)
def init(self, iterative):
# It is mandatory to zero the external momenta.
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
def init(self, iterative):
# It is mandatory to zero the external momenta.
clean_momenta(iterative.pos, iterative.vel, iterative.masses,
iterative.ff.system.cell)
def init(self, iterative):
# It is mandatory to zero the external momenta.
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(iterative.pos.shape[0], iterative.ff.system.cell.nvec)
self.kin = 0.5*iterative.ndof*boltzmann*self.temp
def init(self, iterative):
if not self.restart:
# It is mandatory to zero the external momenta.
clean_momenta(iterative.pos, iterative.vel, iterative.masses, iterative.ff.system.cell)
if iterative.ndof is None:
iterative.ndof = get_ndof_internal_md(iterative.pos.shape[0], iterative.ff.system.cell.nvec)