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):
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)
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)
