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): # 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)