Source code for ase.md.nptberendsen

"""Berendsen NPT dynamics class."""

import numpy as np
import warnings

from ase.md.nvtberendsen import NVTBerendsen
import ase.units as units


[docs]class NPTBerendsen(NVTBerendsen): def __init__(self, atoms, timestep, temperature=None, *, temperature_K=None, pressure=None, pressure_au=None, taut=0.5e3 * units.fs, taup=1e3 * units.fs, compressibility=None, compressibility_au=None, fixcm=True, trajectory=None, logfile=None, loginterval=1, append_trajectory=False): """Berendsen (constant N, P, T) molecular dynamics. This dynamics scale the velocities and volumes to maintain a constant pressure and temperature. The shape of the simulation cell is not altered, if that is desired use Inhomogenous_NPTBerendsen. Parameters: atoms: Atoms object The list of atoms. timestep: float The time step in ASE time units. temperature: float The desired temperature, in Kelvin. temperature_K: float Alias for ``temperature``. pressure: float (deprecated) The desired pressure, in bar (1 bar = 1e5 Pa). Deprecated, use ``pressure_au`` instead. pressure: float The desired pressure, in atomic units (eV/Å^3). taut: float Time constant for Berendsen temperature coupling in ASE time units. Default: 0.5 ps. taup: float Time constant for Berendsen pressure coupling. Default: 1 ps. compressibility: float (deprecated) The compressibility of the material, in bar-1. Deprecated, use ``compressibility_au`` instead. compressibility_au: float The compressibility of the material, in atomic units (Å^3/eV). fixcm: bool (optional) If True, the position and momentum of the center of mass is kept unperturbed. Default: True. trajectory: Trajectory object or str (optional) Attach trajectory object. If *trajectory* is a string a Trajectory will be constructed. Use *None* for no trajectory. logfile: file object or str (optional) If *logfile* is a string, a file with that name will be opened. Use '-' for stdout. loginterval: int (optional) Only write a log line for every *loginterval* time steps. Default: 1 append_trajectory: boolean (optional) Defaults to False, which causes the trajectory file to be overwriten each time the dynamics is restarted from scratch. If True, the new structures are appended to the trajectory file instead. """ NVTBerendsen.__init__(self, atoms, timestep, temperature=temperature, temperature_K=temperature_K, taut=taut, fixcm=fixcm, trajectory=trajectory, logfile=logfile, loginterval=loginterval, append_trajectory=append_trajectory) self.taup = taup self.pressure = self._process_pressure(pressure, pressure_au) if compressibility is not None and compressibility_au is not None: raise TypeError( "Do not give both 'compressibility' and 'compressibility_au'") if compressibility is not None: # Specified in bar, convert to atomic units warnings.warn(FutureWarning( "Specify the compressibility in atomic units.")) self.set_compressibility( compressibility_au=compressibility / (1e5 * units.Pascal)) else: self.set_compressibility(compressibility_au=compressibility_au) def set_taup(self, taup): self.taup = taup def get_taup(self): return self.taup def set_pressure(self, pressure=None, *, pressure_au=None, pressure_bar=None): self.pressure = self._process_pressure(pressure, pressure_bar, pressure_au) def get_pressure(self): return self.pressure def set_compressibility(self, *, compressibility_au): self.compressibility = compressibility_au def get_compressibility(self): return self.compressibility def set_timestep(self, timestep): self.dt = timestep def get_timestep(self): return self.dt def scale_positions_and_cell(self): """ Do the Berendsen pressure coupling, scale the atom position and the simulation cell.""" taupscl = self.dt / self.taup stress = self.atoms.get_stress(voigt=False, include_ideal_gas=True) old_pressure = -stress.trace() / 3 scl_pressure = (1.0 - taupscl * self.compressibility / 3.0 * (self.pressure - old_pressure)) #print("old_pressure", old_pressure, self.pressure) #print("volume scaling by:", scl_pressure) cell = self.atoms.get_cell() cell = scl_pressure * cell self.atoms.set_cell(cell, scale_atoms=True) def step(self, forces=None): """ move one timestep forward using Berenden NPT molecular dynamics.""" NVTBerendsen.scale_velocities(self) self.scale_positions_and_cell() # one step velocity verlet atoms = self.atoms if forces is None: forces = atoms.get_forces(md=True) p = self.atoms.get_momenta() p += 0.5 * self.dt * forces if self.fix_com: # calculate the center of mass # momentum and subtract it psum = p.sum(axis=0) / float(len(p)) p = p - psum self.atoms.set_positions( self.atoms.get_positions() + self.dt * p / self.atoms.get_masses()[:, np.newaxis]) # We need to store the momenta on the atoms before calculating # the forces, as in a parallel Asap calculation atoms may # migrate during force calculations, and the momenta need to # migrate along with the atoms. For the same reason, we # cannot use self.masses in the line above. self.atoms.set_momenta(p) forces = self.atoms.get_forces(md=True) atoms.set_momenta(self.atoms.get_momenta() + 0.5 * self.dt * forces) return forces def _process_pressure(self, pressure, pressure_au): """Handle that pressure can be specified in multiple units. For at least a transition period, Berendsen NPT dynamics in ASE can have the pressure specified in either bar or atomic units (eV/Å^3). Two parameters: pressure: None or float The original pressure specification in bar. A warning is issued if this is not None. pressure_au: None or float Pressure in ev/Å^3. Exactly one of the two pressure parameters must be different from None, otherwise an error is issued. Return value: Pressure in eV/Å^3. """ if (pressure is not None) + (pressure_au is not None) != 1: raise TypeError("Exactly one of the parameters 'pressure'," + " and 'pressure_au' must" + " be given") if pressure is not None: w = ("The 'pressure' parameter is deprecated, please" + " specify the pressure in atomic units (eV/Å^3)" + " using the 'pressure_au' parameter.") warnings.warn(FutureWarning(w)) return pressure * (1e5 * units.Pascal) else: return pressure_au
class Inhomogeneous_NPTBerendsen(NPTBerendsen): """Berendsen (constant N, P, T) molecular dynamics. This dynamics scale the velocities and volumes to maintain a constant pressure and temperature. The size of the unit cell is allowed to change independently in the three directions, but the angles remain constant. Usage: NPTBerendsen(atoms, timestep, temperature, taut, pressure, taup) atoms The list of atoms. timestep The time step. temperature The desired temperature, in Kelvin. taut Time constant for Berendsen temperature coupling. fixcm If True, the position and momentum of the center of mass is kept unperturbed. Default: True. pressure The desired pressure, in bar (1 bar = 1e5 Pa). taup Time constant for Berendsen pressure coupling. compressibility The compressibility of the material, water 4.57E-5 bar-1, in bar-1 mask Specifies which axes participate in the barostat. Default (1, 1, 1) means that all axes participate, set any of them to zero to disable the barostat in that direction. """ def __init__(self, atoms, timestep, temperature=None, *, temperature_K=None, taut=0.5e3 * units.fs, pressure=None, pressure_au=None, taup=1e3 * units.fs, compressibility=None, compressibility_au=None, mask=(1, 1, 1), fixcm=True, trajectory=None, logfile=None, loginterval=1): NPTBerendsen.__init__(self, atoms, timestep, temperature=temperature, temperature_K=temperature_K, taut=taut, taup=taup, pressure=pressure, pressure_au=pressure_au, compressibility=compressibility, compressibility_au=compressibility_au, fixcm=fixcm, trajectory=trajectory, logfile=logfile, loginterval=loginterval) self.mask = mask def scale_positions_and_cell(self): """ Do the Berendsen pressure coupling, scale the atom position and the simulation cell.""" taupscl = self.dt * self.compressibility / self.taup / 3.0 stress = - self.atoms.get_stress(include_ideal_gas=True) if stress.shape == (6,): stress = stress[:3] elif stress.shape == (3, 3): stress = [stress[i][i] for i in range(3)] else: raise ValueError('Cannot use a stress tensor of shape ' + str(stress.shape)) pbc = self.atoms.get_pbc() scl_pressurex = 1.0 - taupscl * (self.pressure - stress[0]) \ * pbc[0] * self.mask[0] scl_pressurey = 1.0 - taupscl * (self.pressure - stress[1]) \ * pbc[1] * self.mask[1] scl_pressurez = 1.0 - taupscl * (self.pressure - stress[2]) \ * pbc[2] * self.mask[2] cell = self.atoms.get_cell() cell = np.array([scl_pressurex * cell[0], scl_pressurey * cell[1], scl_pressurez * cell[2]]) self.atoms.set_cell(cell, scale_atoms=True)