def md(gen='poscar.gen', index=0, totstep=100):
atoms = read(gen, index=index)
atoms.calc = IRFF(atoms=atoms, libfile='ffield.json', rcut=None, nn=True)
# dyn = BFGS(atoms)
dyn = VelocityVerlet(atoms, 0.1 * units.fs) # 5 fs time step.
def printenergy(a=atoms):
"""Function to print the potential, kinetic and total energy"""
natom = len(a)
epot = a.get_potential_energy() / natom
ekin = a.get_kinetic_energy() / natom
T = ekin / (1.5 * units.kB)
try:
assert T <= 8000.0, 'Temperature goes too high!'
except:
print('Temperature goes too high, stop at step %d.' % dyn.nsteps)
dyn.max_steps = dyn.nsteps - 1
# print(a.get_forces())
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, T, epot + ekin))
traj = Trajectory('md.traj', 'w', atoms)
dyn = VelocityVerlet(atoms, 0.1 * units.fs) # 5 fs time step.
dyn.attach(printenergy, interval=1)
dyn.attach(traj.write, interval=1)
dyn.run(totstep)
def ase_md_playground():
geom = AnaPot.get_geom((0.52, 1.80, 0), atoms=("H", ))
atoms = geom.as_ase_atoms()
# ase_calc = FakeASE(geom.calculator)
# from ase.optimize import BFGS
# dyn = BFGS(atoms)
# dyn.run(fmax=0.05)
import ase
from ase import units
from ase.io.trajectory import Trajectory
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.verlet import VelocityVerlet
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
momenta = atoms.get_momenta()
momenta[0, 2] = 0.
# Zero 3rd dimension
atoms.set_momenta(momenta)
dyn = VelocityVerlet(atoms, .005 * units.fs) # 5 fs time step.
def printenergy(a):
"""Function to print the potential, kinetic and total energy"""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
# Now run the dynamics
printenergy(atoms)
traj_fn = 'asemd.traj'
traj = Trajectory(traj_fn, 'w', atoms)
dyn.attach(traj.write, interval=5)
# dyn.attach(bumms().bimms, interval=1)
dyn.run(10000)
printenergy(atoms)
traj.close()
traj = ase.io.read(traj_fn+"@:")#, "r")
pos = [a.get_positions() for a in traj]
from pysisyphus.constants import BOHR2ANG
pos = np.array(pos) / BOHR2ANG
calc = geom.calculator
calc.plot()
ax = calc.ax
ax.plot(*pos[:,0,:2].T)
plt.show()
def test_apply_strain(self):
calc = TersoffScr(**Tersoff_PRB_39_5566_Si_C__Scr)
timestep = 1.0 * units.fs
atoms = ase.io.read('cryst_rot_mod.xyz')
atoms.set_calculator(calc)
# constraints
top = atoms.positions[:, 1].max()
bottom = atoms.positions[:, 1].min()
fixed_mask = ((abs(atoms.positions[:, 1] - top) < 1.0) |
(abs(atoms.positions[:, 1] - bottom) < 1.0))
fix_atoms = FixAtoms(mask=fixed_mask)
# strain
orig_height = (atoms.positions[:, 1].max() -
atoms.positions[:, 1].min())
delta_strain = timestep * 1e-5 * (1 / units.fs)
rigid_constraints = False
strain_atoms = ConstantStrainRate(orig_height, delta_strain)
atoms.set_constraint(fix_atoms)
# dynamics
np.random.seed(0)
simulation_temperature = 300 * units.kB
MaxwellBoltzmannDistribution(atoms, 2.0 * simulation_temperature)
dynamics = VelocityVerlet(atoms, timestep)
def apply_strain(atoms, ConstantStrainRate, rigid_constraints):
ConstantStrainRate.apply_strain(atoms, rigid_constraints)
dynamics.attach(apply_strain, 1, atoms, strain_atoms,
rigid_constraints)
dynamics.run(100)
# tests
if rigid_constraints == True:
answer = 0
temp_answer = 238.2066417638124
else:
answer = 0.013228150080099255
temp_answer = 236.76904696481486
newpos = atoms.get_positions()
current_height = newpos[:, 1].max() - newpos[:, 1].min()
diff_height = (current_height - orig_height)
self.assertAlmostEqual(diff_height, answer)
temperature = (atoms.get_kinetic_energy() /
(1.5 * units.kB * len(atoms)))
self.assertAlmostEqual(temperature, temp_answer)
def test_apply_strain(self):
calc = TersoffScr(**Tersoff_PRB_39_5566_Si_C__Scr)
timestep = 1.0*units.fs
atoms = ase.io.read('cryst_rot_mod.xyz')
atoms.set_calculator(calc)
# constraints
top = atoms.positions[:, 1].max()
bottom = atoms.positions[:, 1].min()
fixed_mask = ((abs(atoms.positions[:, 1] - top) < 1.0) |
(abs(atoms.positions[:, 1] - bottom) < 1.0))
fix_atoms = FixAtoms(mask=fixed_mask)
# strain
orig_height = (atoms.positions[:, 1].max() - atoms.positions[:, 1].min())
delta_strain = timestep*1e-5*(1/units.fs)
rigid_constraints = False
strain_atoms = ConstantStrainRate(orig_height, delta_strain)
atoms.set_constraint(fix_atoms)
# dynamics
np.random.seed(0)
simulation_temperature = 300*units.kB
MaxwellBoltzmannDistribution(atoms, 2.0*simulation_temperature)
dynamics = VelocityVerlet(atoms, timestep)
def apply_strain(atoms, ConstantStrainRate, rigid_constraints):
ConstantStrainRate.apply_strain(atoms, rigid_constraints)
dynamics.attach(apply_strain, 1, atoms, strain_atoms, rigid_constraints)
dynamics.run(100)
# tests
if rigid_constraints == True:
answer = 0
temp_answer = 238.2066417638124
else:
answer = 0.013228150080099255
temp_answer = 236.76904696481486
newpos = atoms.get_positions()
current_height = newpos[:, 1].max() - newpos[:, 1].min()
diff_height = (current_height - orig_height)
self.assertAlmostEqual(diff_height, answer)
temperature = (atoms.get_kinetic_energy()/(1.5*units.kB*len(atoms)))
self.assertAlmostEqual(temperature, temp_answer)
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(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 run_md():
# Use Asap for a huge performance increase if it is installed
use_asap = True
if use_asap:
from asap3 import EMT
size = 10
else:
from ase.calculators.emt import EMT
size = 3
# Set up a crystal
atoms = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol="Cu",
size=(size, size, size),
pbc=True)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.calc = EMT()
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
# We want to run MD with constant energy using the VelocityVerlet algorithm.
dyn = VelocityVerlet(atoms, 5 * units.fs) # 5 fs time step.
traj = Trajectory('cu.traj', 'w', atoms)
dyn.attach(traj.write, interval=10)
def printenergy(a=atoms): # store a reference to atoms in the definition.
epot, ekin = calcenergy(a)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, ekin /
(1.5 * units.kB), epot + ekin))
# Now run the dynamics
dyn.attach(printenergy, interval=10)
printenergy()
dyn.run(200)
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
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
else:
atoms = AtomsReader(args.input_file)[-1]
atoms.set_calculator(qm_pot)
if args.restart:
#delete certain keys so they don't cause problem in write_xyz.
del_keys = ['force','forces', 'forces0']
array_keys = atoms.arrays.keys()
prop_keys = atoms.properties.keys()
for key in del_keys:
if key in array_keys:
del(atoms.arrays[key])
#thermalize atoms
if not args.restart:
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
dynamics = VelocityVerlet(atoms, timestep)
def print_context(ats=atoms, dyn=dynamics):
print 'steps, T', dyn.nsteps, ats.get_kinetic_energy()/(1.5*units.kB*len(ats))
def write_slab(a=atoms):
write_xyz('surf_traj.xyz', a, append=True)
dynamics.attach(print_context, interval=1)
dynamics.attach(write_slab, interval=1)
dynamics.run(nsteps)
dynamics = VelocityVerlet(atoms, params.timestep)
check_force_error = False
if not params.classical:
qmmm_pot.set(calc_weights=True)
dynamics.state_label = 'D'
else:
print 'Initializing LOTF Dynamics'
dynamics = LOTFDynamics(atoms, params.timestep,
params.extrapolate_steps,
check_force_error=check_force_error)
system_timer('init_dynamics')
#Function to update the QM region at the beginning of each extrapolation cycle
if not check_force_error:
if params.extrapolate_steps == 1:
if not params.classical:
dynamics.attach(update_qm_region, 1, dynamics.atoms)
else:
# choose appropriate update function for defects or crack.
# or grainboundary.
print 'Setting Update Function'
if geom =='disloc':
dynamics.set_qm_update_func(update_qm_region)
elif geom =='crack':
dynamics.set_qm_update_func(update_qm_region_crack)
else:
print 'No geometry chosen', 1/0
if check_force_error:
pred_corr_logfile = open(os.path.join(params.rundir, 'pred-corr-error.txt'), 'w')
dynamics.attach(log_pred_corr_errors, 1, dynamics, pred_corr_logfile)
N_c = 16 * np.round(cell_c / (0.25 * 16))
calc = GPAW(gpts=N_c,
nbands=1,
basis='dzp',
setups={'Na': '1'},
txt=name + '_gs.txt')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write(name + '_gs.gpw', mode='all')
del atoms, calc
time.sleep(10)
while not os.path.isfile(name + '_gs.gpw'):
print('Node %d waiting for file...' % world.rank)
time.sleep(10)
world.barrier()
tdcalc = GPAW(name + '_gs.gpw', txt=name + '_td.txt')
tdcalc.forces.reset() #XXX debug
tdcalc.initialize_positions()
atoms = tdcalc.get_atoms()
traj = PickleTrajectory(name + '_td.traj', 'w', atoms)
verlet = VelocityVerlet(atoms,
timestep * 1e-3 * fs,
logfile=paropen(name + '_td.verlet', 'w'),
trajectory=traj)
verlet.attach(Timing(paropen(name + '_td.log', 'w')), ndiv, atoms)
verlet.run(niter)
traj.close()
atoms.set_calculator(qmmm_pot)
#Otherwise it will recover temperature from the previous run.
#Use same random seed so that initialisations are deterministic.
if not args.restart:
print 'Thermalizing atoms'
np.random.seed(42)
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
dynamics = VelocityVerlet(atoms, timestep)
def print_context(ats=atoms, dyn=dynamics):
print 'steps, T', dyn.nsteps, ats.get_kinetic_energy()/(1.5*units.kB*len(ats))
print 'G', get_energy_release_rate(ats)/(units.J/units.m**2)
print 'strain', get_strain(ats)
dynamics.attach(print_context, interval=8)
print 'Running Crack Simulation'
dynamics.run(nsteps)
print 'Crack Simulation Finished'
elif args.lotf:
crack_pos = atoms.info['CrackPos']
r_scale = 1.00894848312
mm_pot = Potential('IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale), param_filename=eam_pot, cutoff_skin=2.0)
#test potential
#quippy using atomic units
atoms.cutoff = 3.0
atoms.set_cutoff(3.0)
atoms.calc_connect()
qmmm_pot = ForceMixingPotential(pot1=mm_pot, pot2=qm_pot, atoms=atoms,
# Describe the interatomic interactions with the Effective Medium Theory
atoms.set_calculator(lammps['ref'])
np.random.seed(42)
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(atoms, 1000 * units.kB)
# We want to run MD with constant energy using the VelocityVerlet algorithm.
dyn = VelocityVerlet(atoms, 1 * units.fs) # 5 fs time step.
def printenergy(a):
"""Function to print the potential, kinetic and total energy"""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
delta = np.max(np.abs(a.get_forces() - lammps['our'].get_forces(a)))
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV d=%.3e' % (epot, ekin, ekin /
(1.5 * units.kB), epot + ekin, delta))
from ase.io.trajectory import Trajectory
traj = Trajectory('example.traj', 'w', atoms)
dyn.attach(traj.write, interval=1)
# Now run the dynamics
printenergy(atoms)
for i in range(100):
dyn.run(1)
printenergy(atoms)
pot = Potential('IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale), param_filename=eam_pot)
defect.set_calculator(pot)
else:
print 'No potential chosen', 1/0
print 'Finding initial dislocation core positions...'
try:
defect.params['core']
except KeyError:
defect.params['core'] = np.array([98.0, 98.0, 1.49])
defect = set_quantum(defect, params.n_core)
MaxwellBoltzmannDistribution(defect, 2.0*sim_T)
if dyn_type =='eam':
dynamics = VelocityVerlet(defect, timestep)
dynamics.attach(pass_print_context(defect, dynamics))
elif dyn_type =='LOTF':
defect.info['core']= np.array([98.0, 98.0, 1.49])
print 'Initializing LOTFDynamics'
verbosity_push(PRINT_VERBOSE)
dynamics = LOTFDynamics(defect, timestep,
params.extrapolate_steps,
check_force_error=False)
dynamics.set_qm_update_func(update_qm_region)
dynamics.attach(pass_print_context(defect, dynamics))
dynamics.attach(traj_writer, print_interval, defect)
else:
print 'No dyn_type chosen', 1/0
trajectory = AtomsWriter('{0}.traj.xyz'.format(input_file))
print 'Running Crack Simulation'
atoms.info['label'] = 'D' # Label for the status line
atoms.info['time'] = dynamics.get_time()/units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5*units.kB*len(atoms)))
atoms.info['strain'] = get_strain(atoms)
atoms.info['G'] = get_energy_release_rate(atoms)/(units.J/units.m**2)
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
dynamics.attach(printstatus)
# Check if the crack has advanced, and stop incrementing the strain if it has
def check_if_cracked(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
# stop straining if crack has advanced more than tip_move_tol
if not atoms.info['is_cracked'] and (crack_pos[0] - orig_crack_pos[0]) > tip_move_tol:
atoms.info['is_cracked'] = True
del atoms.constraints[atoms.constraints.index(strain_atoms)]
dynamics.attach(check_if_cracked, 1, atoms)
# Save frames to the trajectory every `traj_interval` time steps
trajectory = AtomsWriter(traj_file)
dynamics.attach(trajectory, traj_interval, atoms)
def molecular_dynamics(molecule,
calculator,
temperature=300.0,
sample_interval=10,
total_time=10.0,
time_step=0.1,
seed=None):
"""
Run molecular dynamics on a structure
"""
if seed is not None:
np.random.seed(seed)
dt = time_step * ase.units.fs
temp = temperature * ase.units.kB
steps = int(total_time * 1000.0 / time_step)
velocitydistribution.MaxwellBoltzmannDistribution(molecule,
temp,
force_temp=True)
velocitydistribution.Stationary(molecule)
velocitydistribution.ZeroRotation(molecule)
print("Initial temperature from velocities %.2f" %
molecule.get_temperature())
print("Performing %d steps of %f fs for a total time of %f ps" %
(steps, time_step, total_time))
molecule.set_calculator(calculator)
# dyn = Langevin(
# molecule,
# 1.0*ase.units.fs,
# temp,
# friction=0.001,
# logfile='-',
# loginterval=sample_interval
# )
dyn = VelocityVerlet(molecule,
dt,
logfile='-',
loginterval=sample_interval,
trajectory='dynamics.traj')
md_path = []
count_steps = 0
ave_temp = 0
def log_md_path(atoms):
nonlocal md_path
nonlocal count_steps
nonlocal ave_temp
if count_steps % sample_interval == 0:
md_path.append(atoms.copy())
ave_temp += atoms.get_temperature()
count_steps += 1
start_time = time.time()
dyn.attach(log_md_path, 10, molecule)
dyn.run(steps)
end_time = time.time()
print("Time to sample dynamics %.2f s" % (end_time - start_time))
#ave_temp /= len(md_path)
#print("Total MD time %.2f" % (steps / 1000.0))
#print("Average Temperature during MD %.2f" % (ave_temp))
return md_path
atoms.info['label'] = 'D' # Label for the status line
atoms.info['time'] = dynamics.get_time() / units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5 * units.kB * len(atoms)))
atoms.info['strain'] = get_strain(atoms)
atoms.info['G'] = get_energy_release_rate(atoms) / (units.J / units.m**2)
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
dynamics.attach(printstatus)
def atom_straining(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
# keep straining until the crack tip has advanced to tip_move_tol
if not atoms.info['is_cracked'] and (crack_pos[0] -
orig_crack_pos[0]) < tip_move_tol:
strain_atoms.apply_strain(atoms)
elif not atoms.info['is_cracked']:
atoms.info['is_cracked'] = True
dynamics.attach(atom_straining, 1, atoms)
# Save frames to the trajectory every `traj_interval` time steps
def run_md(atoms, id):
# Read settings
settings = read_settings_file()
# Use KIM for potentials from OpenKIM
use_kim = True
# Use Asap for a huge performance increase if it is installed
use_asap = True
# Create a copy of the initial atoms object for future reference
old_atoms = copy.deepcopy(atoms)
# Describe the interatomic interactions with OpenKIM potential
if use_kim: # use KIM potential
atoms.calc = KIM(
"LJ_ElliottAkerson_2015_Universal__MO_959249795837_003")
else: # otherwise, default to asap3 LennardJones
atoms.calc = LennardJones([18], [0.010323], [3.40],
rCut=6.625,
modified=True)
# Set the momenta corresponding to temperature from settings file
MaxwellBoltzmannDistribution(atoms, settings['temperature'] * units.kB)
# Select integrator
if settings['ensemble'] == "NVE":
from ase.md.verlet import VelocityVerlet
dyn = VelocityVerlet(atoms, settings['time_step'] * units.fs)
elif settings['ensemble'] == "NVT":
from ase.md.langevin import Langevin
dyn = Langevin(atoms, settings['time_step'] * units.fs,
settings['temperature'] * units.kB,
settings['friction'])
traj = Trajectory('ar.traj', 'w', atoms)
dyn.attach(traj.write, interval=1000)
# Identity number given as func. parameter to keep track of properties
# Number of decimals for most calculated properties
decimals = settings['decimals']
# Calculation and writing of properties
properties.initialize_properties_file(atoms, id, decimals)
dyn.attach(properties.calc_properties, 100, old_atoms, atoms, id, decimals)
# unnecessary, used for logging md runs
# we should write some kind of logger for the MD
def logger(a=atoms): # store a reference to atoms in the definition.
"""Function to print the potential, kinetic and total energy."""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
t = ekin / (1.5 * units.kB)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, t, epot + ekin))
# Running the dynamics
dyn.attach(logger, interval=1000)
logger()
dyn.run(settings['max_steps'])
return atoms
Y2 = []
Z2 = []
def dump_positions():
(x1, y1, z1), (x2, y2, z2) = planets.get_positions()
X1.append(x1)
Y1.append(y1)
Z1.append(z1)
X2.append(x2)
Y2.append(y2)
Z2.append(z2)
dyn = VelocityVerlet(planets, timestep=0.01 * fs)
dyn.attach(dump_positions)
dyn.run(20000)
###############################################################################
# Now let's plot the trajectory to see what we get:
if __name__ == '__main__':
plt.clf()
plt.plot(X1, Y1, label='C')
plt.plot(X2, Y2, label='H')
plt.legend()
plt.axes().set_aspect('equal')
plt.show()
###############################################################################
# To check the correctness of this dynamics, we use pytest to test if it is on
else:
i += 1
c = FixAtoms(indices = array)
atoms.set_constraint(c)
# relax with Quasi Newtonian
qn = QuasiNewton(atoms, trajectory='qn.traj')
qn.run(fmax=0.001)
write('qn.final.xyz', atoms)
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(atoms, 300*units.kB)
print 'Removing linear momentum and angular momentum'
Stationary(atoms) # zero linear momentum
ZeroRotation(atoms) # zero angular momentum
# We want to run MD using the VelocityVerlet algorithm.
dyn = VelocityVerlet(atoms, 0.1*units.fs, trajectory='moldyn4.traj') # save trajectory.
#Function to print the potential, kinetic and total energy.
def printenergy(a=atoms): #store a reference to atoms in the definition.
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print ("Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) Etot = %.3feV" %
(epot, ekin, ekin/(1.5*units.kB), epot+ekin))
dyn.attach(printenergy, interval=10)
# Now run the dynamics
printenergy()
dyn.run(2000)
param_filename=eam_pot)
defect.set_calculator(pot)
else:
print 'No potential chosen', 1 / 0
print 'Finding initial dislocation core positions...'
try:
defect.params['core']
except KeyError:
defect.params['core'] = np.array([98.0, 98.0, 1.49])
defect = set_quantum(defect, params.n_core)
MaxwellBoltzmannDistribution(defect, 2.0 * sim_T)
if dyn_type == 'eam':
dynamics = VelocityVerlet(defect, timestep)
dynamics.attach(pass_print_context(defect, dynamics))
elif dyn_type == 'LOTF':
defect.info['core'] = np.array([98.0, 98.0, 1.49])
print 'Initializing LOTFDynamics'
verbosity_push(PRINT_VERBOSE)
dynamics = LOTFDynamics(defect,
timestep,
params.extrapolate_steps,
check_force_error=False)
dynamics.set_qm_update_func(update_qm_region)
dynamics.attach(pass_print_context(defect, dynamics))
dynamics.attach(traj_writer, print_interval, defect)
else:
print 'No dyn_type chosen', 1 / 0
trajectory = AtomsWriter('{0}.traj.xyz'.format(input_file))
velocities_t1 = velocities
coordinates_t1 = coordinates
force_up_t1 = force_up_t2
force_down_t1 = force_down_t2
force_mid_t1 = force_mid_t2
# condition to avoid hops immediately after each other
if skip_next:
if skip_count == 3:
skip_count = 0
skip_next = False
else:
skip_count += 1
# if the hop was accepted
if hop:
# decrement j_md because we made one MD step back
j_md -= 1
skip_next = True
hop = False
# increment global MD counter
j_md += 1
"""Launcher for molecular dynamics"""
# run MD for n_md steps with TSH module
dyn.attach(tsh, interval=1)
dyn.run(n_md)
# close data files
df.close()
#df2.close()
log_format = ('%(label)-4s%(time)12.1f%(temperature)12.6f'+
'%(strain)12.4f%(crack_pos_x)12.2f (%(d_crack_pos_x)+5.2f)')
atoms.info['label'] = 'D' # Label for the status line
atoms.info['time'] = dynamics.get_time()/units.fs
atoms.info['temperature'] = get_temperature(atoms)
atoms.info['strain'] = get_strain(atoms)
# FIXME no local virial in TS, need another way to track the crack
atoms.info['crack_pos_x'] = 0.
atoms.info['d_crack_pos_x'] = 0.
print log_format % atoms.info
dynamics.attach(printstatus)
# Check if the crack has advanced, and stop incrementing the strain if it has
def check_if_cracked(atoms):
#crack_pos = find_tip_stress_field(atoms)
# FIXME TS has no local virial
crack_pos = [0.0, 0.0, 0.0]
# stop straining if crack has advanced more than tip_move_tol
if (not atoms.info['is_cracked'] and
(crack_pos[0] - orig_crack_pos[0]) > params.tip_move_tol):
atoms.info['is_cracked'] = True
del atoms.constraints[atoms.constraints.index(strain_atoms)]
dynamics.attach(check_if_cracked, 1, atoms)
atoms.info['label'] = 'D' # Label for the status line
atoms.info['time'] = dynamics.get_time() / units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5 * units.kB * len(atoms)))
atoms.info['strain'] = get_strain(atoms)
atoms.info['G'] = get_energy_release_rate(atoms) / (units.J / units.m**2)
crack_pos = find_tip_stress_field(atoms)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
dynamics.attach(printstatus)
# Check if the crack has advanced enough and apply strain if it has not
def check_if_crack_advanced(atoms):
crack_pos = find_tip_stress_field(atoms)
# strain if crack has not advanced more than tip_move_tol
if crack_pos[0] - orig_crack_pos[0] < params.tip_move_tol:
strain_atoms.apply_strain(atoms)
dynamics.attach(check_if_crack_advanced, 1, atoms)
# Save frames to the trajectory every `traj_interval` time steps
trajectory = NetCDFTrajectory(params.traj_file, mode='w')
log_format = ('%(label)-4s%(time)12.1f%(temperature)12.6f'+
'%(strain)12.5f%(G)12.4f%(crack_pos_x)12.2f (%(d_crack_pos_x)+5.2f)')
atoms.info['label'] = 'D' # Label for the status line
atoms.info['time'] = dynamics.get_time()/units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5*units.kB*len(atoms)))
atoms.info['strain'] = get_strain(atoms)
atoms.info['G'] = get_energy_release_rate(atoms)/(units.J/units.m**2)
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
dynamics.attach(printstatus)
def check_if_cracked(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
# stop straining if crack has advanced more than tip_move_tol
if not atoms.info['is_cracked'] and (crack_pos[0] - orig_crack_pos[0]) > tip_move_tol:
atoms.info['is_cracked'] = True
del atoms.constraints[atoms.constraints.index(strain_atoms)]
dynamics.attach(check_if_cracked, 1, atoms)
trajectory = AtomsWriter(traj_file)
dynamics.attach(trajectory, traj_interval, atoms)
dynamics.run(nsteps)
def run_md(atoms, id, settings_fn):
"""The function does Molecular Dyanamic simulation (MD) on a material, given by argument atoms.
Parameters:
atoms (obj): an atoms object defined by class in ase. This is the material which MD
will run on.
id (int): an identifying number for the material.
Returns:
obj:atoms object defined in ase, is returned.
"""
# Read settings
settings = read_settings_file(settings_fn)
initial_unitcell_atoms = copy.deepcopy(atoms)
# Scale atoms object, cubic
size = settings['supercell_size']
atoms = atoms * size * (1, 1, 1)
# atoms = atoms * (size,size,size)
#print(atoms.get_chemical_symbols())
N = len(atoms.get_chemical_symbols())
# Use KIM for potentials from OpenKIM
use_kim = settings['use_kim']
# Use Asap for a huge performance increase if it is installed
use_asap = True
# Create a copy of the initial atoms object for future reference
old_atoms = copy.deepcopy(atoms)
# Describe the interatomic interactions with OpenKIM potential
if use_kim: # use KIM potential
atoms.calc = KIM(
"LJ_ElliottAkerson_2015_Universal__MO_959249795837_003")
else: # otherwise, default to asap3 LennardJones
atoms.calc = LennardJones([18], [0.010323], [3.40],
rCut=6.625,
modified=True)
# Set the momenta corresponding to temperature from settings file
MaxwellBoltzmannDistribution(atoms, settings['temperature'] * units.kB)
# Select integrator
if settings['ensemble'] == "NVE":
from ase.md.verlet import VelocityVerlet
dyn = VelocityVerlet(atoms, settings['time_step'] * units.fs)
elif settings['ensemble'] == "NVT":
from ase.md.langevin import Langevin
dyn = Langevin(atoms, settings['time_step'] * units.fs,
settings['temperature'] * units.kB,
settings['friction'])
interval = settings['interval']
# Creates trajectory files in directory trajectory_files
traj = Trajectory("trajectory_files/" + id + ".traj", 'w', atoms)
dyn.attach(traj.write, interval=interval)
# Number of decimals for most calculated properties.
decimals = settings['decimals']
# Boolean indicating if the material is monoatomic.
monoatomic = len(set(atoms.get_chemical_symbols())) == 1
# Calculation and writing of properties
properties.initialize_properties_file(atoms, initial_unitcell_atoms, id,
decimals, monoatomic)
dyn.attach(properties.calc_properties, 100, old_atoms, atoms, id, decimals,
monoatomic)
# unnecessary, used for logging md runs
# we should write some kind of logger for the MD
def logger(a=atoms): # store a reference to atoms in the definition.
"""Function to print the potential, kinetic and total energy."""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
t = ekin / (1.5 * units.kB)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, t, epot + ekin))
# Running the dynamics
dyn.attach(logger, interval=interval)
#logger()
#dyn.run(settings['max_steps'])
# check for thermal equilibrium
counter = 0
equilibrium = False
for i in range(round(settings['max_steps'] /
settings['search_interval'])): # hyperparameter
epot, ekin_pre, etot, t = properties.energies_and_temp(atoms)
# kör steg som motsvarar säg 5 fs
dyn.run(settings['search_interval']) # hyperparamter
epot, ekin_post, etot, t = properties.energies_and_temp(atoms)
#print(abs(ekin_pre-ekin_post) / math.sqrt(N))
#print(counter)
if (abs(ekin_pre - ekin_post) / math.sqrt(N)) < settings['tolerance']:
counter += 1
else:
counter = 0
if counter > settings['threshold']: # hyperparameter
print("reached equilibrium")
equilibrium = True
break
if equilibrium:
dyn.run(settings['max_steps'])
properties.finalize_properties_file(atoms, id, decimals, monoatomic)
else:
properties.delete_properties_file(id)
raise RuntimeError("MD did not find equilibrium")
return atoms
atoms.info['label'] = 'D' # Label for the status line
atoms.info['time'] = dynamics.get_time() / units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5 * units.kB * len(atoms)))
atoms.info['strain'] = get_strain(atoms)
atoms.info['G'] = get_energy_release_rate(atoms) / (units.J / units.m**2)
crack_pos = find_tip_stress_field(atoms)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
dynamics.attach(printstatus)
# Check if the crack has advanced, and stop incrementing the strain if it has
def check_if_cracked(atoms):
crack_pos = find_tip_stress_field(atoms)
# stop straining if crack has advanced more than tip_move_tol
if (not atoms.info['is_cracked']
and (crack_pos[0] - orig_crack_pos[0]) > params.tip_move_tol):
atoms.info['is_cracked'] = True
del atoms.constraints[atoms.constraints.index(strain_atoms)]
dynamics.attach(check_if_cracked, 1, atoms)
atoms.set_pbc(False)
atoms.center(vacuum=6.0)
atoms.set_velocities(np.zeros_like(atoms.get_positions()))
cell_c = np.sum(atoms.get_cell()**2, axis=1)**0.5
N_c = 16 * np.round(cell_c / (0.25 * 16))
calc = GPAW(gpts=N_c, nbands=1, basis='dzp', setups={'Na': '1'},
txt=name + '_gs.txt')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write(name + '_gs.gpw', mode='all')
del atoms, calc
time.sleep(10)
while not os.path.isfile(name + '_gs.gpw'):
print 'Node %d waiting for file...' % world.rank
time.sleep(10)
world.barrier()
tdcalc = GPAW(name + '_gs.gpw', txt=name + '_td.txt')
tdcalc.forces.reset() #XXX debug
tdcalc.initialize_positions()
atoms = tdcalc.get_atoms()
traj = PickleTrajectory(name + '_td.traj', 'w', atoms)
verlet = VelocityVerlet(atoms, timestep * 1e-3 * fs,
logfile=paropen(name + '_td.verlet', 'w'),
trajectory=traj)
verlet.attach(Timing(paropen(name + '_td.log', 'w')), ndiv, atoms)
verlet.run(niter)
traj.close()
size = 3
# Set up a crystal
atoms = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol="Cu",
size=(size, size, size),
pbc=True)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.calc = EMT()
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
# We want to run MD with constant energy using the VelocityVerlet algorithm.
dyn = VelocityVerlet(atoms, 5 * units.fs) # 5 fs time step.
def printenergy(a=atoms): # store a reference to atoms in the definition.
"""Function to print the potential, kinetic and total energy."""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
# Now run the dynamics
dyn.attach(printenergy, interval=10)
printenergy()
dyn.run(200)
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)