def md_run(
parent_dataset,
dft_calculator,
starting_image,
temp,
dt,
count,
label,
ensemble="NVE",
):
slab = starting_image.copy()
slab.set_calculator(AMPOnlineCalc(parent_dataset, dft_calculator, 3))
# MaxwellBoltzmannDistribution(slab, temp * units.kB)
if ensemble == "nvtberendsen":
dyn = NVTBerendsen(slab,
dt * ase.units.fs,
temp,
taut=300 * ase.units.fs)
traj = ase.io.Trajectory(label + ".traj", "w", slab)
dyn.attach(traj.write, interval=1)
dyn.run(count - 1)
if atom.position[i] > cell[i,i]-self.margin:
atom.momentum[i] = -abs(atom.momentum[i])
if __name__ == '__main__':
# test
from ase.cluster.cubic import FaceCenteredCubic
from ase.calculators.emt import EMT
from ase.md.nvtberendsen import NVTBerendsen
from ase.io.trajectory import Trajectory
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution, Stationary, ZeroRotation
from ase.units import fs, kB
atoms = FaceCenteredCubic(
'Pt', [(1, 0, 0), (1, 1, 0), (1, 1, 1)], [2, 3, 1], 4.09)
atoms.center(vacuum=5)
atoms.set_calculator( EMT() )
T = 8000 # K -- try to vaporize
MaxwellBoltzmannDistribution(atoms, kB*T)
Stationary(atoms)
ZeroRotation(atoms)
#dyn = NVTBerendsen(atoms, 1*fs, T, 500*fs, logfile='-')
dyn = NVTBerendsen(atoms, 1*fs, T, 500*fs, logfile='-')
traj = Trajectory('borders_test.traj', 'w', atoms)
dyn.attach(traj.write, interval=10)
fr = Freeze(atoms)
#fr = Mirror(atoms)
dyn.attach( fr, interval=20 )
dyn.run(5000)
traj.close()
calc = GAP(rcut=6.0)
nsw, pstress, tebeg, potim, _ = read_incar()
my_atoms = read('POSCAR', format='vasp')
my_atoms.set_calculator(calc)
"""
for NVT
"""
#print(tebeg,'tebeg')
dyn = NVTBerendsen(my_atoms,
timestep=potim * fs,
temperature=tebeg,
taut=0.5 * 1000 * fs,
trajectory='ase.traj')
dyn.attach(MDLogger(dyn,
my_atoms,
'OUTCAR',
header=True,
stress=True,
pstress=pstress,
peratom=False,
mode="w"),
interval=1)
dyn.run(steps=nsw)
atoms_lat = my_atoms.cell
atoms_pos = my_atoms.positions
atoms_symbols = my_atoms.get_chemical_symbols()
element, ele = get_ele_dict(atoms_symbols)
write_contcar(element, ele, atoms_lat, atoms_pos)
si.set_calculator(calc)
# geometry optimization
si = optimize(si, box=True)
print('equlirum cell para: ', si.get_cell()[0][0])
print('equlirum energy: ', si.get_potential_energy())
print('equlirum stress', -si.get_stress() / units.GPa)
# Build the 2*2*2 supercell
atoms = si * 2
atoms.set_calculator(calc)
print(atoms)
# NVT MD simulation
dyn = NVTBerendsen(atoms,
p.time_step * units.fs,
p.temperature,
taut=p.taut * units.fs)
MaxwellBoltzmannDistribution(atoms, p.temperature * units.kB)
dyn.attach(MDLogger(dyn,
atoms,
'md.log',
header=True,
stress=False,
mode="w"),
interval=p.save_interval)
traj = Trajectory('md.traj', 'w', atoms)
dyn.attach(traj.write, interval=p.save_interval)
dyn.run(p.run_step)
