def test_read_dftb_velocities():
atoms = Atoms('H2')
filename = 'geo_end.xyz'
with open(filename, 'w') as fd:
fd.write(geo_end_xyz)
# Velocities (in Angstrom / ps) of the last MD iteration
# The first 4 columns are the atom charge and coordinates
read_dftb_velocities(atoms, filename=filename)
velocities = np.linspace(-1, 2, num=6).reshape(2, 3)
velocities /= 1e-12 * second
assert np.allclose(velocities, atoms.get_velocities())
Driver_Velocities_empty='<<+ "velocities.txt"',
Driver_Steps=500,
Driver_KeepStationary='Yes',
Driver_TimeStep=8.26,
Driver_Thermostat_='Berendsen',
Driver_Thermostat_Temperature=0.00339845142, # 800 degC
Driver_Thermostat_CouplingStrength=0.01)
write_dftb_velocities(atoms, 'velocities.txt')
atoms.calc = calculator_NVE
atoms.get_potential_energy() # run NVE ensemble using DFTB+'s own driver
atoms = read('geo_end.gen')
write('after_NVE.xyz', atoms)
read_dftb_velocities(atoms, filename='geo_end.xyz')
write_dftb_velocities(atoms, 'velocities.txt')
os.system('mv geo_end.xyz geo_end_NVE.xyz')
atoms.calc = calculator_NVT
atoms.get_potential_energy() # run NVT ensemble using DFTB+'s own driver
atoms = read('geo_end.gen')
write('after_NVT.xyz', atoms)
read_dftb_velocities(atoms, filename='geo_end.xyz')
write_dftb_velocities(atoms, 'velocities.txt')
os.system('mv geo_end.xyz geo_end_NVT.xyz')
# to watch:
# ase gui geo_end_NVE.xyz geo_end_NVT.xyz
Driver_Thermostat_='Berendsen',
Driver_Thermostat_Temperature=0.00339845142, # 800 deg Celcius
# Driver_Thermostat_Temperature=0.0, # 0 deg Kelvin
Driver_Thermostat_CouplingStrength=0.01)
write_dftb_velocities(test, 'velocities.txt')
os.system('rm md.log.* md.out* geo_end*xyz')
test.set_calculator(calculator_NVE)
dyn = VelocityVerlet(test, 0.000 * fs) # fs time step.
dyn.attach(MDLogger(dyn, test, 'md.log.NVE', header=True, stress=False,
peratom=False, mode='w'), interval=1)
dyn.run(1) # run NVE ensemble using DFTB's own driver
test = read('geo_end.gen')
write('test.afterNVE.xyz', test)
read_dftb_velocities(test, filename='geo_end.xyz')
write_dftb_velocities(test, 'velocities.txt')
os.system('mv md.out md.out.NVE')
os.system('mv geo_end.xyz geo_end_NVE.xyz')
test.set_calculator(calculator_NVT)
os.system('rm md.log.NVT')
dyn.attach(MDLogger(dyn, test, 'md.log.NVT', header=True, stress=False,
peratom=False, mode='w'), interval=1)
dyn.run(1) # run NVT ensemble using DFTB's own driver
test = read('geo_end.gen')
read_dftb_velocities(test, filename='geo_end.xyz')
os.system('mv md.out md.out.NVT')
os.system('mv geo_end.xyz geo_end_NVT.xyz')
Driver_Thermostat_='Berendsen',
Driver_Thermostat_Temperature=0.00339845142, # 800 deg Celcius
# Driver_Thermostat_Temperature=0.0, # 0 deg Kelvin
Driver_Thermostat_CouplingStrength=0.01)
write_dftb_velocities(test, 'velocities.txt')
os.system('rm md.log.* md.out* geo_end*xyz')
test.set_calculator(calculator_NVE)
dyn = VelocityVerlet(test, 0.000 * fs) # fs time step.
dyn.attach(MDLogger(dyn, test, 'md.log.NVE', header=True, stress=False,
peratom=False, mode='w'), interval=1)
dyn.run(1) # run NVE ensemble using DFTB's own driver
test = read('geo_end.gen')
write('test.afterNVE.xyz', test)
read_dftb_velocities(test, filename='geo_end.xyz')
write_dftb_velocities(test, 'velocities.txt')
os.system('mv md.out md.out.NVE')
os.system('mv geo_end.xyz geo_end_NVE.xyz')
test.set_calculator(calculator_NVT)
os.system('rm md.log.NVT')
dyn.attach(MDLogger(dyn, test, 'md.log.NVT', header=True, stress=False,
peratom=False, mode='w'), interval=1)
dyn.run(1) # run NVT ensemble using DFTB's own driver
test = read('geo_end.gen')
read_dftb_velocities(test, filename='geo_end.xyz')
os.system('mv md.out md.out.NVT')
os.system('mv geo_end.xyz geo_end_NVT.xyz')