def init_md(self, name, time_step=0.5, temp_init=300, temp_bath=None, reset=False, interval=1):
"""
Initialize an ase molecular dynamics trajectory. The logfile needs to be specifies, so that old trajectories
are not overwritten. This functionality can be used to subsequently carry out equilibration and production.
Args:
name (str): Basic name of logfile and trajectory
time_step (float): Time step in fs (default=0.5)
temp_init (float): Initial temperature of the system in K (default is 300)
temp_bath (float): Carry out Langevin NVT dynamics at the specified temperature. If set to None, NVE
dynamics are performed instead (default=None)
reset (bool): Whether dynamics should be restarted with new initial conditions (default=False)
interval (int): Data is stored every interval steps (default=1)
"""
# If a previous dynamics run has been performed, don't reinitialize velocities unless explicitely requested
# via restart=True
if not self.dynamics or reset:
self._init_velocities(temp_init=temp_init)
# Set up dynamics
if temp_bath is None:
self.dynamics = VelocityVerlet(self.molecule, time_step * units.fs)
else:
self.dynamics = Langevin(self.molecule, time_step * units.fs, temp_bath * units.kB, 0.01)
# Create monitors for logfile and a trajectory file
logfile = os.path.join(self.working_dir, "%s.log" % name)
trajfile = os.path.join(self.working_dir, "%s.traj" % name)
logger = MDLogger(self.dynamics, self.molecule, logfile, stress=False, peratom=False, header=True, mode='a')
trajectory = Trajectory(trajfile, 'w', self.molecule)
# Attach monitors to trajectory
self.dynamics.attach(logger, interval=interval)
self.dynamics.attach(trajectory.write, interval=interval)
def _molecular_dynamics(self, step, N):
"""Performs a molecular dynamics simulation, until mdmin is
exceeded. If resuming, the file number (md%05i) is expected."""
mincount = 0
energies, oldpositions = [], []
thermalized = False
if not thermalized:
self.MaxwellBoltzmannDistribution(N,
temp=self.temperature * kB,
force_temp=True)
traj = io.Trajectory('md.traj', 'a', self.atoms)
dyn = VelocityVerlet(self.atoms, dt=self.timestep * units.fs)
log = MDLogger(dyn, self.atoms, 'md.log',
header=True, stress=False, peratom=False)
dyn.attach(log, interval=1)
dyn.attach(traj, interval=1)
os.remove('md.log')
os.remove('md.traj')
while mincount < self.mdmin:
dyn.run(1)
energies.append(self.atoms.get_potential_energy())
passedmin = self.passedminimum(energies)
if passedmin:
mincount += 1
oldpositions.append(self.atoms.positions.copy())
# Reset atoms to minimum point.
self.atoms.positions = oldpositions[passedmin[0]]
def _molecular_dynamics(self, resume=None):
"""Performs a molecular dynamics simulation, until mdmin is
exceeded. If resuming, the file number (md%05i) is expected."""
self._log('msg', 'Molecular dynamics: md%05i' % self._counter)
mincount = 0
energies, oldpositions = [], []
thermalized = False
if resume:
self._log('msg', 'Resuming MD from md%05i.traj' % resume)
if os.path.getsize('md%05i.traj' % resume) == 0:
self._log(
'msg', 'md%05i.traj is empty. Resuming from '
'qn%05i.traj.' % (resume, resume - 1))
atoms = io.read('qn%05i.traj' % (resume - 1), index=-1)
else:
images = io.Trajectory('md%05i.traj' % resume, 'r')
for atoms in images:
energies.append(atoms.get_potential_energy())
oldpositions.append(atoms.positions.copy())
passedmin = self._passedminimum(energies)
if passedmin:
mincount += 1
self._atoms.set_momenta(atoms.get_momenta())
thermalized = True
self._atoms.positions = atoms.get_positions()
self._log('msg',
'Starting MD with %i existing energies.' % len(energies))
if not thermalized:
MaxwellBoltzmannDistribution(self._atoms,
temp=self._temperature * units.kB,
force_temp=True)
traj = io.Trajectory('md%05i.traj' % self._counter, 'a', self._atoms)
self._constrain()
dyn = NPT(self._atoms,
timestep=self._timestep * units.fs,
temperature=self._temperature * units.kB,
externalstress=self._externalstress,
ttime=self._ttime * units.fs,
pfactor=self._pfactor * units.fs**2)
# dyn = NPTber(self._atoms, timestep=self._timestep * units.fs, temperature=self._temperature, fixcm=True, pressure=self._pressure, taut=self._taut * units.fs, taup=self._taup * units.fs, compressibility=self._compressibility)
log = MDLogger(dyn,
self._atoms,
'md%05i.log' % self._counter,
header=True,
stress=False,
peratom=False)
dyn.attach(log, interval=1)
dyn.attach(traj, interval=1)
while mincount < self._mdmin:
# self._constrain()
dyn.run(1)
# del self._atoms.constraints
energies.append(self._atoms.get_potential_energy())
passedmin = self._passedminimum(energies)
if passedmin:
mincount += 1
oldpositions.append(self._atoms.positions.copy())
# Reset atoms to minimum point.
self._atoms.positions = oldpositions[passedmin[0]]
def __init__(self, atoms, timestep, trajectory, logfile=None,
loginterval=1):
Dynamics.__init__(self, atoms, logfile=None, trajectory=trajectory)
self.dt = timestep
# Store data locally except on parallel simulations
self._localdata = not getattr(atoms, "parallel", False)
if logfile:
self.attach(MDLogger(dyn=self, atoms=atoms, logfile=logfile),
interval=loginterval)
def create_system(self,
name,
time_step=1.0,
temp=300,
temp_init=None,
restart=False,
store=1,
nvt=False,
friction=0.001):
"""
Parameters
-----------
name : str
Name for output files.
time_step : float, optional
Time step in fs for simulation.
temp : float, optional
Temperature in K for NVT simulation.
temp_init : float, optional
Optional different temperature for initialization than thermostate set at.
restart : bool, optional
Determines whether simulation is restarted or not,
determines whether new velocities are initialized.
store : int, optional
Frequency at which output is written to log files.
nvt : bool, optional
Determines whether to run NVT simulation, default is False.
friction : float, optional
friction coefficient in fs^-1 for Langevin integrator
"""
if temp_init is None: temp_init = temp
if not self.md or restart:
MaxwellBoltzmannDistribution(self.mol, temp_init * units.kB)
if not nvt:
self.md = VelocityVerlet(self.mol, time_step * units.fs)
else:
self.md = Langevin(self.mol, time_step * units.fs, temp * units.kB,
friction / units.fs)
logfile = os.path.join(self.tmp, "{}.log".format(name))
trajfile = os.path.join(self.tmp, "{}.traj".format(name))
logger = MDLogger(self.md,
self.mol,
logfile,
stress=False,
peratom=False,
header=True,
mode="a")
trajectory = Trajectory(trajfile, "w", self.mol)
self.md.attach(logger, interval=store)
self.md.attach(trajectory.write, interval=store)
def _molecular_dynamics(self, N, resume=None):
"""Performs a molecular dynamics simulation, until mdmin is
exceeded. If resuming, the file number (md%05i) is expected."""
self._log('msg', 'Molecular dynamics: md%05i' % self._counter)
mincount = 0
energies, oldpositions = [], []
thermalized = False
if resume:
self._log('msg', 'Resuming MD from md%05i.traj' % resume)
if os.path.getsize('md.traj') == 0:
self._log('msg', 'md%05i.traj is empty. Resuming from '
'qn%05i.traj.' % (resume, resume - 1))
atoms = io.read('qn.traj', index=-1)
else:
images = io.Trajectory('md.traj' % resume, 'r')
for atoms in images:
energies.append(atoms.get_potential_energy())
oldpositions.append(atoms.positions.copy())
passedmin = self._passedminimum(energies)
if passedmin:
mincount += 1
self._atoms.set_momenta(atoms.get_momenta())
thermalized = True
self._atoms.positions = atoms.get_positions()
self._log('msg', 'Starting MD with %i existing energies.' %
len(energies))
if not thermalized:
self.MaxwellBoltzmannDistribution(self._atoms,
N,
temp=self._temperature * units.kB,
force_temp=True)
if (self._counter > 1):
os.remove('md.log')
os.remove('md.traj')
traj = io.Trajectory('md.traj', 'a', self._atoms)
dyn = VelocityVerlet(self._atoms, dt=self._timestep * units.fs)
log = MDLogger(dyn, self._atoms, 'md.log',
header=True, stress=False, peratom=False)
dyn.attach(log, interval=1)
dyn.attach(traj, interval=1)
while mincount < self._mdmin:
dyn.run(1)
energies.append(self._atoms.get_potential_energy())
passedmin = self._passedminimum(energies)
if passedmin:
mincount += 1
oldpositions.append(self._atoms.positions.copy())
# Reset atoms to minimum point.
self._atoms.positions = oldpositions[passedmin[0]]
def MD(self):
"""Molecular Dynamic"""
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase import units
from ase.md import MDLogger
from ase.io.trajectory import PickleTrajectory
from ase.md.langevin import Langevin
from ase.md.verlet import VelocityVerlet
dyndrivers = {
'Langevin': Langevin,
'None': VelocityVerlet,
}
useAsap = False
mol = self.mol
temperature = self.definedParams['temperature']
init_temperature = self.definedParams['init_temperature']
time_step = self.definedParams['time_step']
nstep = self.definedParams['nstep']
nprint = self.definedParams['nprint']
thermostat = self.definedParams['thermostat']
prop_file = os.path.join(self.definedParams['workdir'],
self.definedParams['output_prefix'] + '.out')
traj_file = os.path.join(self.definedParams['workdir'],
self.definedParams['output_prefix'] + '.traj')
MaxwellBoltzmannDistribution(mol, init_temperature * units.kB)
if thermostat == 'None':
dyn = VelocityVerlet(mol, time_step * units.fs)
elif thermostat == 'Langevin':
dyn = Langevin(mol, time_step * units.fs, temperature * units.kB,
0.01)
else:
raise ImplementationError(
method, 'Thermostat is not implemented in the MD function')
#Function to print the potential, kinetic and total energy
traj = PickleTrajectory(traj_file, "a", mol)
dyn.attach(MDLogger(dyn, mol, prop_file), interval=nprint)
dyn.attach(traj.write, interval=nprint)
dyn.run(nstep)
traj.close()
def md_calculation(fcp_file):
from ase import units
from ase.io.trajectory import Trajectory
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.langevin import Langevin
from ase.md import MDLogger
if 'fcc' in fcp_file:
ref_cell = read(ref_fcc)
P = np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]])
P *= 3
atoms = make_supercell(ref_cell, P)
else:
raise ValueError("Unknown phase")
fcp = ForceConstantPotential.read(fcp_file)
fcs = fcp.get_force_constants(atoms)
calc = ForceConstantCalculator(fcs)
atoms.set_calculator(calc)
temperature = 200
number_of_MD_steps = 100
time_step = 5 # in fs
dump_interval = 10
traj_file = "data/md_" + fcp_file.split('.')[0] + '{}.traj'.format(
temperature)
log_file = "data/md_log_{}.log".format(temperature)
dyn = Langevin(atoms, time_step * units.fs, temperature * units.kB, 0.02)
logger = MDLogger(dyn,
atoms,
log_file,
header=True,
stress=False,
peratom=True,
mode='w')
traj_writer = Trajectory(traj_file, 'w', atoms)
dyn.attach(logger, interval=dump_interval)
dyn.attach(traj_writer.write, interval=dump_interval)
# run MD
MaxwellBoltzmannDistribution(atoms, temperature * units.kB)
dyn.run(number_of_MD_steps)
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')
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
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)
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")
test.set_calculator(calculator_NVT)
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)
from ase.build import graphene_nanoribbon
from ase.visualize import view
from ase import units
from ase.md.verlet import VelocityVerlet
from ase.calculators.emt import EMT
from ase.md.langevin import Langevin
from ase.md import MDLogger
from ase.md.npt import NPT
import numpy as np
gnrb = graphene_nanoribbon(20, 20, type="armchair", saturated=True, vacuum=3.5)
view(gnrb)
gnrb.set_calculator(EMT())
dyn = VelocityVerlet(gnrb, dt=5.0 * units.fs)
# dyn = Langevin(gnrb, 5 * units.fs, units.kB * 123, 0.002)
stress = 2
# dyn = NPT(gnrb, 5*units.fs, 300*units.kB, stress, 25*units.fs, 75*units.fs)
dyn.attach(MDLogger(dyn,
gnrb,
'md2.log',
header=True,
stress=False,
peratom=True,
mode="w"),
interval=1)
dyn.run(100)
# view(gnrb)