def test_write_dftb_velocities():
atoms = Atoms('H2')
velocities = np.linspace(-1, 2, num=6).reshape(2, 3)
atoms.set_velocities(velocities)
write_dftb_velocities(atoms, filename='velocities.txt')
velocities = np.loadtxt('velocities.txt') * Bohr / AUT
assert np.allclose(velocities, atoms.get_velocities())
label='h2o',
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_O='p',
Hamiltonian_MaxAngularMomentum_H='s',
Driver_='VelocityVerlet',
Driver_MDRestartFrequency=5,
Driver_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)
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_O='"p"',
Hamiltonian_MaxAngularMomentum_H='"s"',
Driver_='VelocityVerlet',
Driver_MDRestartFrequency=5,
Driver_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 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')
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_O='"p"',
Hamiltonian_MaxAngularMomentum_H='"s"',
Driver_='VelocityVerlet',
Driver_MDRestartFrequency=5,
Driver_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 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')
def run_dftb(self, gen='poscar.gen'):
if self.np == 1:
system('dftb+>dftb.out')
else:
system('mpirun -n %d dftb+>dftb.out' % self.np)
def get_thermal(self, out='dftb.out'):
e, p, t = get_dftb_energy(out=out)
return e, p, t
def close(self):
print('- Hugstate calculation compeleted.')
if __name__ == '__main__':
if isfile('dftb.traj'):
A = read('dftb.traj', index=-1)
write_dftb_velocities(A, 'velocities')
A.write('poscar.gen')
v = 'velocities'
else:
v = None
''' evergy (mdRestart) to write MD trajectories i.e. positions and velocities
when task completed, can use " ase gui dftb.traj to see the MD results"
'''
dftb = DFTB(pressure=None,
dT=5.0,
ncpu=40,
skf_dir='/home/leno/scisoft/3ob-3-1/')
dftb.nvt(T=2500, compress=0.996, mdRestart=10, velocities=v)