def integrate_atoms(
self,
atoms,
traj_file,
n_steps,
save_interval,
steps=0,
timestep=5.0,
traj_dir="trajs",
convert=False,
):
if not os.path.exists(traj_dir):
os.mkdir(traj_dir)
traj_file = os.path.join(traj_dir, traj_file)
if not os.path.exists(traj_file):
traj = Trajectory(traj_file, "w")
print("Creating trajectory {}...".format(traj_file))
dyn = VelocityVerlet(atoms, timestep=timestep * units.fs)
count = n_steps // save_interval
for i in range(count):
dyn.run(save_interval)
energy = atoms.get_total_energy()
forces = atoms.get_forces()
traj.write(atoms)
steps += save_interval
print("Steps: {}, total energy: {}".format(steps, energy))
else:
print("Trajectory {} already exists!".format(traj_file))
if convert:
self.convert_trajectory(traj_file)
return steps, traj_file
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 test_rattle():
i = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
for calc in [
TIP3P(),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i)
]:
dimer = s22('Water_dimer')
for m in [0, 3]:
dimer.set_angle(m + 1, m, m + 2, angleHOH)
dimer.set_distance(m, m + 1, rOH, fix=0)
dimer.set_distance(m, m + 2, rOH, fix=0)
fixOH1 = [(3 * i, 3 * i + 1) for i in range(2)]
fixOH2 = [(3 * i, 3 * i + 2) for i in range(2)]
fixHH = [(3 * i + 1, 3 * i + 2) for i in range(2)]
dimer.set_constraint(FixBondLengths(fixOH1 + fixOH2 + fixHH))
dimer.calc = calc
e = dimer.get_potential_energy()
md = VelocityVerlet(dimer,
8.0 * units.fs,
trajectory=calc.name + '.traj',
logfile=calc.name + '.log',
loginterval=5)
md.run(25)
de = dimer.get_potential_energy() - e
assert abs(de - -0.028) < 0.001
def __init__(self, atoms, timestep=None, trajectory=None, dt=None,
**kwargs):
VelocityVerlet.__init__(self, atoms, timestep, trajectory, dt=dt)
OTF.__init__(self, **kwargs)
self.md_engine = 'VelocityVerlet'
def test_rattle_linear():
"""Test RATTLE and QM/MM for rigid linear acetonitrile."""
import numpy as np
from ase import Atoms
from ase.calculators.acn import (ACN, m_me, r_cn, r_mec, sigma_me, sigma_c,
sigma_n, epsilon_me, epsilon_c, epsilon_n)
from ase.calculators.qmmm import SimpleQMMM, EIQMMM, LJInteractionsGeneral
from ase.md.verlet import VelocityVerlet
from ase.constraints import FixLinearTriatomic
import ase.units as units
sigma = np.array([sigma_me, sigma_c, sigma_n])
epsilon = np.array([epsilon_me, epsilon_c, epsilon_n])
i = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3)
for calc in [
ACN(),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()),
EIQMMM([0, 1, 2], ACN(), ACN(), i)
]:
dimer = Atoms('CCNCCN', [(-r_mec, 0, 0), (0, 0, 0), (r_cn, 0, 0),
(r_mec, 3.7, 0), (0, 3.7, 0),
(-r_cn, 3.7, 0)])
masses = dimer.get_masses()
masses[::3] = m_me
dimer.set_masses(masses)
fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
dimer.set_constraint(fixd)
dimer.calc = calc
d1 = dimer[:3].get_all_distances()
d2 = dimer[3:].get_all_distances()
e = dimer.get_potential_energy()
md = VelocityVerlet(dimer,
2.0 * units.fs,
trajectory=calc.name + '.traj',
logfile=calc.name + '.log',
loginterval=20)
md.run(100)
de = dimer.get_potential_energy() - e
assert np.all(abs(dimer[:3].get_all_distances() - d1) < 1e-10)
assert np.all(abs(dimer[3:].get_all_distances() - d2) < 1e-10)
assert abs(de - -0.005) < 0.001
def maketraj(atoms, t, nstep):
e = [atoms.get_potential_energy()]
print "Shape of force:", atoms.get_forces().shape
dyn = VelocityVerlet(atoms, 5 * units.fs)
for i in range(nstep):
dyn.run(10)
energy = atoms.get_potential_energy()
e.append(energy)
if ismaster:
print "Energy: ", energy
if t is not None:
t.write()
return e
def maketraj(atoms, t, nstep):
e = [atoms.get_potential_energy()]
print "Shape of force:", atoms.get_forces().shape
dyn = VelocityVerlet(atoms, 5*units.fs)
for i in range(nstep):
dyn.run(10)
energy = atoms.get_potential_energy()
e.append(energy)
if ismaster:
print "Energy: ", energy
if t is not None:
t.write()
return e
def test_md(cp2k_factory):
calc = cp2k_factory.calc(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
MaxwellBoltzmannDistribution(atoms,
temperature_K=0.5 * 300,
force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
dyn = VelocityVerlet(atoms, 0.5 * units.fs)
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert abs(energy_start - energy_end) < 1e-4
def set_lattice_params(self, md='NVE', **kwargs):
#self.lattice_model.set(**kwargs)
self.lattice_temperature = kwargs['lattice_temperature']
self.lattice_time_step = kwargs['lattice_time_step']
self.lattice_friction = kwargs['lattice_friction']
if md == 'Langevin':
self._lattice_dyn = Langevin(self.atoms,
self.lattice_time_step,
self.lattice_temperature,
self.lattice_friction,
trajectory='LattHist.traj')
elif md == 'NVE':
self._lattice_dyn = VelocityVerlet(self.atoms,
dt=self.lattice_time_step,
trajectory='LattHist.traj')
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 constant_energy(nuclear_charges, coordinates, dump=None, calculator=None):
"""
"""
if calculator is None:
# LOAD AND SET MODEL
parameters = {}
parameters["offset"] = -97084.83100465109
parameters["sigma"] = 10.0
alphas = np.load(FILENAME_ALPHAS)
X = np.load(FILENAME_REPRESENTATIONS)
Q = np.load(FILENAME_CHARGES)
alphas = np.array(alphas, order="F")
X = np.array(X, order="F")
calculator = QMLCalculator(parameters, X, Q, alphas)
molecule = ase.Atoms(nuclear_charges, coordinates)
molecule.set_calculator(calculator)
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(molecule, 200 * units.kB)
# We want to run MD with constant energy using the VelocityVerlet algorithm.
dyn = VelocityVerlet(molecule, 1 * units.fs) # 5 fs time step.
# if dump is not None:
# traj = Trajectory(dump, 'w', molecule)
# dyn.attach(traj.write, interval=5)
def printenergy(a=molecule,
t=None): # 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('pEpot = %.2feV Ekin = %.2feV (T=%3.0fK) '
'Etot = %.4feV t=%.4f' % (epot, ekin, ekin /
(1.5 * units.kB), epot + ekin, t))
for i in range(10):
start = time.time()
dyn.run(0)
end = time.time()
printenergy(t=end - start)
return
def run(self):
MaxwellBoltzmannDistribution(self.atoms, self.intT * units.kB)
self.dyn = VelocityVerlet(self.atoms,
self.time_step * units.fs,
trajectory='md.traj')
def printenergy(a=self.atoms):
epot_ = a.get_potential_energy()
r = a.calc.r.numpy()
i_ = np.where(np.logical_and(r < self.rtole * self.ro, r > 0.0001))
n = len(i_[0])
self.Epot.append(epot_)
self.epot = epot_ / self.natom
self.ekin = a.get_kinetic_energy() / self.natom
self.T = self.ekin / (1.5 * units.kB)
self.step = self.dyn.nsteps
print('Step %d Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (self.step, self.epot, self.ekin, self.T,
self.epot + self.ekin))
try:
assert n == 0 and self.T < self.Tmax, 'Atoms too closed!'
except:
for _ in i_:
print('atoms pair', _)
print('Atoms too closed or temperature too high, stop at %d.' %
self.step)
self.dyn.max_steps = self.dyn.nsteps - 1
# traj = Trajectory('md.traj', 'w', self.atoms)
self.dyn.attach(printenergy, interval=1)
# self.dyn.attach(traj.write,interval=1)
self.dyn.run(self.totstep)
def set_initial_velocities(self, distribution, energy):
distribution(self.atoms, energy)
try:
os.remove(self.traj)
except:
pass
try:
os.remove(self._log)
except:
pass
VelocityVerlet.__init__(self,
atoms=self.atoms,
timestep=self.dt,
trajectory=self.traj,
loginterval=1,
logfile=self._log,
append_trajectory=False)
self.update_properties()
def test_md(cp2k_factory):
calc = cp2k_factory.calc(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
# Run MD
MaxwellBoltzmannDistribution(atoms, 0.5 * 300 * units.kB, force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
dyn = VelocityVerlet(atoms, 0.5 * units.fs)
#def print_md():
# energy = atoms.get_potential_energy() + atoms.get_kinetic_energy()
# print("MD total-energy: %.10feV" % energy)
#dyn.attach(print_md, interval=1)
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert energy_start - energy_end < 1e-4
print('passed test "H2_MD"')
def get_ANN_energy(input_file):
(structure_file, T, dt, md_steps, print_steps, trajectory_file,
potentials) = parse_input(input_file)
# atomic structure
atoms = ase.io.read(structure_file, format='vasp')
# ANN calculator
calc = ANNCalculator(potentials)
atoms.set_calculator(calc)
# initialize velocities
MaxwellBoltzmannDistribution(atoms, temp=T * units.kB)
# initialize MD
md = VelocityVerlet(atoms, dt * units.fs, trajectory=trajectory_file)
print("# {:5s} {:15s} {:15s} {:7s} {:15s}".format("step", "E_pot", "E_kin",
"T", "E_tot"))
printenergy(0, atoms)
istep = 0
for i in range(int(md_steps / print_steps)):
md.run(steps=print_steps)
istep += print_steps
printenergy(istep, atoms)
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 main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
# Run MD
MaxwellBoltzmannDistribution(atoms, 0.5 * 300 * units.kB, force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
dyn = VelocityVerlet(atoms, 0.5 * units.fs)
#def print_md():
# energy = atoms.get_potential_energy() + atoms.get_kinetic_energy()
# print("MD total-energy: %.10feV" % energy)
#dyn.attach(print_md, interval=1)
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert energy_start - energy_end < 1e-4
print('passed test "H2_MD"')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
# Run MD
MaxwellBoltzmannDistribution(atoms, 0.5 * 300 * units.kB, force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
dyn = VelocityVerlet(atoms, 0.5 * units.fs)
#def print_md():
# energy = atoms.get_potential_energy() + atoms.get_kinetic_energy()
# print("MD total-energy: %.10feV" % energy)
#dyn.attach(print_md, interval=1)
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert energy_start - energy_end < 1e-4
print('passed test "H2_MD"')
def run_md_Morse(Morse_parameters, A0, steps=10000, trajectory="md.traj"):
hbar_fs = (ase.units._hbar / ase.units._e) * 1.E15
D, a, R0, frequency = Morse_parameters[0:4]
r0 = R0
calculator = MorsePotential2(a=a, D=D, r0=r0)
#calculator = MorsePotential(rho0=6.0, epsilon=2.0, r0=1.0)
period = (hbar_fs / frequency) / (2 * pi)
pos = 1 * (r0 + A0)
atoms = Atoms("HH", positions=[[0, 0, 0], [pos, 0, 0]], masses=[1.0, 1.0])
constr = FixAtoms(indices=[0])
atoms.set_constraint(constr)
atoms.set_calculator(calculator)
# def V(d):
# atoms.set_positions([[0,0,0],[d,0,0]])
# return atoms.get_potential_energy()
# r_plot = linspace(-4.0,4.0,1000)
# V_plot = array([V(d) for d in r_plot])
# plt.plot(r_plot,V_plot)
# plt.show()
dynamics = VelocityVerlet(atoms,
dt=(period / 20.) * ase.units.fs,
trajectory=trajectory)
dynamics.run(20000)
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 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 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)
def run(self):
self.dyn = VelocityVerlet(self.atoms,
self.time_step * units.fs,
trajectory='md.traj')
def printenergy(a=self.atoms):
epot_ = a.get_potential_energy()
r = a.calc.r.detach().numpy()
i_ = np.where(np.logical_and(r < self.rtole * self.ro, r > 0.0001))
n = len(i_[0])
if len(self.Epot) == 0:
dE_ = 0.0
else:
dE_ = abs(epot_ - self.Epot[-1])
self.Epot.append(epot_)
self.epot = epot_ / self.natom
self.ekin = a.get_kinetic_energy() / self.natom
self.T = self.ekin / (1.5 * units.kB)
self.step = self.dyn.nsteps
print('Step %d Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (self.step, self.epot, self.ekin, self.T,
self.epot + self.ekin))
try:
if self.CheckDE:
assert n == 0 and dE_ < self.dEstop, 'Atoms too closed or Delta E too high!'
else:
assert n == 0 and self.T < self.Tmax, 'Atoms too closed or Temperature goes too high!'
except:
# for _ in i_:
# print('atoms pair',_)
print(
'Atoms too closed or Temperature goes too high, stop at %d.'
% self.step)
self.dyn.max_steps = self.dyn.nsteps - 1
# traj = Trajectory('md.traj', 'w', self.atoms)
self.dyn.attach(printenergy, interval=1)
# self.dyn.attach(traj.write,interval=1)
self.dyn.run(self.totstep)
def serve_md(nuclear_charges, coordinates, calculator=None, temp=None):
"""
"""
if calculator is None:
parameters = {}
parameters["offset"] = -97084.83100465109
parameters["sigma"] = 10.0
alphas = np.load(FILENAME_ALPHAS)
X = np.load(FILENAME_REPRESENTATIONS)
Q = np.load(FILENAME_CHARGES, allow_pickle=True)
alphas = np.array(alphas, order="F")
X = np.array(X, order="F")
calculator = QMLCalculator(parameters, X, Q, alphas)
# SET MOLECULE
molecule = ase.Atoms(nuclear_charges, coordinates)
molecule.set_calculator(calculator)
# SET ASE MD
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(molecule, 200 * units.kB)
time = 0.5
if temp is None:
# We want to run MD with constant energy using the VelocityVerlet algorithm.
dyn = VelocityVerlet(molecule, time * units.fs) # 1 fs time step.
else:
dyn = NVTBerendsen(molecule, time*units.fs, temp, time*units.fs, fixcm=False)
# SET AND SERVE NARUPA MD
imd = ASEImdServer(dyn)
while True:
imd.run(10)
print("")
dump_xyz(molecule, tmpdir + "snapshot.xyz")
return
def test_gfn2xtb_velocityverlet():
"""Perform molecular dynamics with GFN2-xTB and Velocity Verlet Integrator"""
thr = 1.0e-5
atoms = Atoms(
symbols="NHCHC2H3OC2H3ONHCH3",
positions=np.array([
[1.40704587284727, -1.26605342016611, -1.93713466561923],
[1.85007200612454, -0.46824072777417, -1.50918242392545],
[-0.03362432532150, -1.39269245193812, -1.74003582081606],
[-0.56857009928108, -1.01764444489068, -2.61263467107342],
[-0.44096297340282, -2.84337808903410, -1.48899734014499],
[-0.47991761226058, -0.55230954385212, -0.55520222968656],
[-1.51566045903090, -2.89187354810876, -1.32273881320610],
[-0.18116520746778, -3.45187805987944, -2.34920431470368],
[0.06989722340461, -3.23298998903001, -0.60872832703814],
[-1.56668253918793, 0.00552120970194, -0.52884675001441],
[1.99245341064342, -1.73097165236442, -3.08869239114486],
[3.42884244212567, -1.30660069291348, -3.28712665743189],
[3.87721962540768, -0.88843123009431, -2.38921453037869],
[3.46548545761151, -0.56495308290988, -4.08311788302584],
[4.00253374168514, -2.16970938132208, -3.61210068365649],
[1.40187968630565, -2.43826111827818, -3.89034127398078],
[0.40869198386066, -0.49101709352090, 0.47992424955574],
[1.15591901335007, -1.16524842262351, 0.48740266650199],
[0.00723492494701, 0.11692276177442, 1.73426297572793],
[0.88822128447468, 0.28499001838229, 2.34645658013686],
[-0.47231557768357, 1.06737634000561, 1.52286682546986],
[-0.70199987915174, -0.50485938116399, 2.28058247845421],
]),
)
calc = XTB(method="GFN2-xTB", cache_api=False)
atoms.set_calculator(calc)
dyn = VelocityVerlet(atoms, timestep=1.0 * fs)
dyn.run(20)
assert approx(atoms.get_potential_energy(), thr) == -896.9772346260584
assert approx(atoms.get_kinetic_energy(), thr) == 0.022411127028842362
atoms.calc.set(cache_api=True)
dyn.run(20)
assert approx(atoms.get_potential_energy(), thr) == -896.9913862530841
assert approx(atoms.get_kinetic_energy(), thr) == 0.036580471363852810
def train_pes_by_tempering(atoms,
gp,
cutoff,
ttime,
calculator=None,
model=None,
dt=2.,
ediff=0.01,
volatile=None,
target_temperature=1000.,
stages=1,
equilibration=5,
rescale_velocities=1.05,
pressure=None,
stress_equilibration=5,
rescale_cell=1.01,
randomize=True,
algorithm='fastfast',
name='model',
overwrite=True,
traj='tempering.traj',
logfile='leapfrog.log'):
assert rescale_velocities > 1 and rescale_cell > 1
if model is not None:
if type(model) == str:
model = PosteriorPotentialFromFolder(model)
if gp is None:
gp = model.gp
if atoms.get_velocities() is None:
t = target_temperature
MaxwellBoltzmannDistribution(atoms, t * units.kB)
Stationary(atoms)
ZeroRotation(atoms)
dyn = VelocityVerlet(atoms, dt * units.fs, trajectory=traj)
dyn = Leapfrog(dyn,
gp,
cutoff,
calculator=calculator,
model=model,
ediff=ediff,
volatile=volatile,
algorithm=algorithm,
logfile=logfile)
t = 0
T = '{} (instant)'.format(atoms.get_temperature())
checkpoints = np.linspace(0, ttime, stages + 1)[1:]
for k, target_t in enumerate(checkpoints):
print('stage: {}, time: {}, target time: {}, (temperature={})'.format(
k, t, target_t, T))
while t < target_t:
spu, e, T, s = dyn.run_updates(equilibration)
t += spu * equilibration * dt
dyn.rescale_velocities(
rescale_velocities if T < target_temperature else 1. /
rescale_velocities)
if pressure is not None:
spu, e, T, s = dyn.run_updates(stress_equilibration)
t += spu * stress_equilibration * dt
p = -s[:3].mean() / units.Pascal
# figure out factor
dp = p - pressure
factor = (rescale_cell if dp > 0 else 1. / rescale_cell)
if randomize:
factor = 1 + np.random.uniform(0, 1) * (factor - 1)
# apply rescaling
dyn.rescale_cell(factor)
if k == stages - 1:
dyn.model.to_folder(name,
info='temperature: {}'.format(T),
overwrite=overwrite)
else:
dyn.model.to_folder('{}_{}'.format(name, k),
info='temperature: {}'.format(T),
overwrite=overwrite)
return dyn.get_atoms(), dyn.model
# Describe the interatomic interactions with the Effective Medium Theory
atoms.set_calculator(EMT())
# Do a quick relaxation of the cluster
qn = QuasiNewton(atoms)
qn.run(0.001, 10)
# Set the momenta corresponding to T=1200K
MaxwellBoltzmannDistribution(atoms, 1200 * units.kB)
Stationary(atoms) # zero linear momentum
ZeroRotation(atoms) # zero angular momentum
# We want to run MD using the VelocityVerlet algorithm.
# Save trajectory:
dyn = VelocityVerlet(atoms, 5 * units.fs, trajectory='moldyn4.traj')
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))
dyn.attach(printenergy, interval=10)
# Now run the dynamics
printenergy()
dyn.run(2000)
strain_atoms = ConstantStrainRate(orig_height,
params.strain_rate * params.timestep)
atoms.set_constraint([fix_atoms, strain_atoms])
atoms.set_calculator(params.calc)
# ********* Setup and run MD ***********
# Set the initial temperature to 2*simT: it will then equilibriate to
# simT, by the virial theorem
MaxwellBoltzmannDistribution(atoms, 2.0 * params.sim_T)
# Initialise the dynamical system
dynamics = VelocityVerlet(atoms, params.timestep)
# Print some information every time step
def printstatus():
if dynamics.nsteps == 1:
print """
State Time/fs Temp/K Strain G/(J/m^2) CrackPos/A D(CrackPos)/A
---------------------------------------------------------------------------------"""
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
dimer = Atoms('CCNCCN', [(-r_mec, 0, 0), (0, 0, 0), (r_cn, 0, 0),
(r_mec, 3.7, 0), (0, 3.7, 0), (-r_cn, 3.7, 0)])
masses = dimer.get_masses()
masses[::3] = m_me
dimer.set_masses(masses)
fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
dimer.set_constraint(fixd)
dimer.calc = calc
d1 = dimer[:3].get_all_distances()
d2 = dimer[3:].get_all_distances()
e = dimer.get_potential_energy()
md = VelocityVerlet(dimer,
2.0 * units.fs,
trajectory=calc.name + '.traj',
logfile=calc.name + '.log',
loginterval=20)
md.run(100)
de = dimer.get_potential_energy() - e
assert np.all(abs(dimer[:3].get_all_distances() - d1) < 1e-10)
assert np.all(abs(dimer[3:].get_all_distances() - d2) < 1e-10)
assert abs(de - -0.005) < 0.001
qmmm_pot = ForceMixingCarvingCalculator(atoms, qm_region_mask,
mm_pot, qm_pot,
buffer_width=qm_outer_radius,
pbc_type=[False, False, True])
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
from asap3 import EMT
size = 10
else:
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.set_calculator(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.
#Function to print the potential, kinetic and total energy
def printenergy(a):
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)
for i in range(20):
dyn.run(10)
printenergy(atoms)
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')
test.set_calculator(calculator_NVT)
os.system('rm md.log.NVT')
dyn.attach(MDLogger(dyn, test, 'md.log.NVT', header=True, stress=False,
dist = 0.001
energy += self.A / dist**self.alpha
return energy
def __repr__(self):
return 'Repulsion potential'
def copy(self):
return CentralRepulsion(self, R=self.R, A=self.A, alpha=self.alpha)
if __name__ == '__main__':
from ase.cluster.cubic import FaceCenteredCubic
from ase.calculators.emt import EMT
from ase.md.verlet import VelocityVerlet
from ase.units import fs
atoms = FaceCenteredCubic('Ag', [(1, 0, 0)], [1], 4.09)
atoms.center(10)
atoms.set_calculator(EMT())
c = ConstantForce(10, [0, 1, 0]) # y=dircted force
atoms.set_constraint(c)
md = VelocityVerlet(atoms, 1*fs, trajectory='cf_test.traj',
logfile='-')
md.run(100)
# from ase.visualize import view
# view(atoms)
# *** Milestone 3.1 -- exit early - we don't want to run the classical MD! ***
import sys
sys.exit(0)
# **** no changes compared to run_crack_classical.py below here yet ****
# ********* Setup and run MD ***********
# Set the initial temperature to 2*simT: it will then equilibriate to
# simT, by the virial theorem
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
# Initialise the dynamical system
dynamics = VelocityVerlet(atoms, timestep)
# Print some information every time step
def printstatus():
if dynamics.nsteps == 1:
print """
State Time/fs Temp/K Strain G/(J/m^2) CrackPos/A D(CrackPos)/A
---------------------------------------------------------------------------------"""
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)))
r_scale = 1.00894848312
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))
atoms.set_constraint([fix_atoms, strain_atoms])
atoms.set_calculator(params.calc)
# ********* Setup and run MD ***********
# Set the initial temperature to 2*simT: it will then equilibrate to
# simT, by the virial theorem
MaxwellBoltzmannDistribution(atoms, 2.0*params.sim_T)
p = atoms.get_momenta()
p[np.where(fixed_mask)] = 0
atoms.set_momenta(p)
# Initialise the dynamical system
dynamics = VelocityVerlet(atoms, params.timestep)
# dynamics = Langevin(atoms, params.timestep, params.sim_T * units.kB, 1e-4, fixcm=True)
# Print some information every time step
def printstatus():
if dynamics.nsteps == 1:
print """
State Time/fs Temp/K Strain G/(J/m^2) CrackPos/A D(CrackPos)/A
---------------------------------------------------------------------------------"""
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)
epot = atoms.get_potential_energy()
print >>stdout, "Potential energy:", epot
ReportTest("Initial potential energy", epot, -301358.3, 0.5)
etot = epot + atoms.get_kinetic_energy()
if 0:
if cpulayout:
traj = ParallelNetCDFTrajectory("parallel.nc", atoms)
else:
traj = NetCDFTrajectory("serial.nc", atoms)
traj.Add("PotentialEnergies")
traj.Update()
traj.Close()
print "Trajectory done"
dyn = VelocityVerlet(atoms, 3*units.fs)
etot2 = None
for i in range(5):
dyn.run(15)
newetot = atoms.get_potential_energy()+ atoms.get_kinetic_energy()
print >>stdout, "Total energy:", newetot
temp = atoms.get_kinetic_energy() / (1.5*units.kB*natoms)
print >>stdout, "Temp:", temp, "K"
if etot2 == None:
ReportTest("Total energy (first step)", newetot, etot, 40.0)
etot2=newetot
else:
ReportTest(("Total energy (step %d)" % (i+1,)),
newetot, etot2, 20.0)
print >>stdout, " *** This test completed ***"
# pass
def __repr__(self):
return 'Push atoms out of the cell back to the cell'
def copy(self):
return ConstantForce(a=self.index, force=self.force)
if __name__ == '__main__':
from ase.cluster.cubic import FaceCenteredCubic
from ase.calculators.emt import EMT
from ase.md.verlet import VelocityVerlet
from ase.units import fs
from constantforce import ConstantForce
atoms = FaceCenteredCubic(
'Ag', [(1, 0, 0)], [1], 4.09)
atoms.center(10)
atoms.pbc = True
atoms.set_calculator( EMT() )
cf = ConstantForce( 10, [0,1,0] ) # y=dircted force
ic = ImprisonConstraint()
atoms.set_constraint( [cf, ic] )
md = VelocityVerlet( atoms, 1*fs, trajectory = 'cf_test.traj', logfile='-' )
md.run(200)
#~ from ase.visualize import view
#~ view(atoms)
def update_atoms(self):
pass
def set_atoms(self, atoms):
self.atoms = atoms
self.update_atoms()
if __name__ == '__main__':
from ase import Atoms
atoms = Atoms(symbols='CeO', cell=[2, 2, 5], positions=np.array([[0.0, 0.0, 0.0], [0.0, 0.0, 2.4935832]]))
atoms[0].charge = +4
atoms[1].charge = -2
calc = Buck({('Ce', 'O'): (1176.3, 0.381, 0.0)})
#calc = Buck( {('Ce', 'O'): (0.0, 0.149, 0.0)} )
atoms.set_calculator(calc)
print('Epot = ', atoms.get_potential_energy())
print('Force = ', atoms.get_forces())
from ase.md.verlet import VelocityVerlet
dyn = VelocityVerlet(atoms, dt=0.1*units.fs, trajectory='test.traj', logfile='-')
dyn.run(1000)
print('coodrs = ', atoms.get_positions())
from ase.visualize import view
view(atoms)
def learn_pes_by_tempering(atoms,
gp,
cutoff,
ttime,
calculator=None,
model=None,
dt=2.,
ediff=0.01,
volatile=None,
target_temperature=1000.,
stages=1,
equilibration=5,
rescale_velocities=1.05,
pressure=None,
stress_equilibration=5,
rescale_cell=1.01,
eps='random',
algorithm='fastfast',
name='model',
overwrite=True,
traj='tempering.traj',
logfile='leapfrog.log'):
"""
pressure (hydrostatic):
defined in units of Pascal and is equal to -(trace of stress tensor)/3
eps:
if 'random', strain *= a random number [0, 1)
if a positive float, strain *= 1-e^(-|dp/p|/eps) i.e. eps ~ relative p fluctuations
else, no action
"""
assert rescale_velocities > 1 and rescale_cell > 1
if pressure is not None:
warnings.warn('rescaling cell is not robust!')
if model is not None:
if type(model) == str:
model = PosteriorPotentialFromFolder(model)
if gp is None:
gp = model.gp
if atoms.get_velocities() is None:
t = target_temperature
MaxwellBoltzmannDistribution(atoms, t * units.kB)
Stationary(atoms)
ZeroRotation(atoms)
dyn = VelocityVerlet(atoms, dt * units.fs, trajectory=traj)
dyn = Leapfrog(dyn,
gp,
cutoff,
calculator=calculator,
model=model,
ediff=ediff,
volatile=volatile,
algorithm=algorithm,
logfile=logfile)
t = 0
T = '{} (instant)'.format(atoms.get_temperature())
checkpoints = np.linspace(0, ttime, stages + 1)[1:]
for k, target_t in enumerate(checkpoints):
print('stage: {}, time: {}, target time: {}, (temperature={})'.format(
k, t, target_t, T))
while t < target_t:
spu, e, T, s = dyn.run_updates(equilibration)
t += spu * equilibration * dt
dyn.rescale_velocities(
rescale_velocities if T < target_temperature else 1. /
rescale_velocities)
if pressure is not None:
spu, e, T, s = dyn.run_updates(stress_equilibration)
t += spu * stress_equilibration * dt
p = -s[:3].mean() / units.Pascal
# figure out strain
dp = p - pressure
strain = (rescale_cell if dp > 0 else 1. / rescale_cell) - 1
if eps is 'random':
strain *= np.random.uniform()
elif type(eps) == float and eps > 0 and abs(p) > 0:
strain *= 1 - np.exp(-np.abs(dp / p) / eps)
# apply strain
dyn.strain_atoms(np.eye(3) * strain)
if k == stages - 1:
dyn.model.to_folder(name,
info='temperature: {}'.format(T),
overwrite=overwrite)
else:
dyn.model.to_folder('{}_{}'.format(name, k),
info='temperature: {}'.format(T),
overwrite=overwrite)
return dyn.get_atoms(), dyn.model
def test(temp, frict):
output = file('Langevin.dat', 'w')
# Make a small perturbation of the momenta
atoms.set_momenta(1e-6 * np.random.random([len(atoms), 3]))
print 'Initializing ...'
predyn = VelocityVerlet(atoms, 0.5)
predyn.run(2500)
dyn = Langevin(atoms, timestep, temp, frict)
print ''
print ('Testing Langevin dynamics with T = %f eV and lambda = %f' %
(temp, frict))
ekin = atoms.get_kinetic_energy()/len(atoms)
print ekin
output.write('%.8f\n' % ekin)
print 'Equilibrating ...'
# Initial guesses for least-squares fit
a = 0.04
b = 2*frict
c = temp
params = (a,b,c)
fitdata = [(0, 2.0 / 3.0 * ekin)]
tstart = time.time()
for i in xrange(1,nequil+1):
dyn.run(nminor)
ekin = atoms.get_kinetic_energy() / len(atoms)
fitdata.append((i*nminor*timestep, 2.0/3.0 * ekin))
if usescipy and i % nequilprint == 0:
(params, chisq) = leastSquaresFit(targetfunc, params, fitdata)
print '%.6f T_inf = %.6f (goal: %f), tau = %.2f, k = %.6f' % \
(ekin, params[2], temp, 1.0/params[1], params[0])
output.write('%.8f\n' % ekin)
tequil = time.time() - tstart
print 'This took %s minutes.' % (tequil / 60)
output.write('&\n')
assert abs(temp-params[2]) < 0.25*temp, 'Least-squares fit is way off'
assert nequil*nminor*timestep > 3.0/params[1], 'Equiliberation was too short'
fitdata = np.array(fitdata)
print 'Recording statistical data - this takes ten times longer!'
temperatures = []
tstart = time.time()
for i in xrange(1,nsteps+1):
dyn.run(nminor)
ekin = atoms.get_kinetic_energy() / len(atoms)
temperatures.append(2.0/3.0 * ekin)
if i % nprint == 0:
tnow = time.time() - tstart
tleft = (nsteps-i) * tnow / i
print '%.6f (time left: %.1f minutes)' % (ekin, tleft/60)
output.write('%.8f\n' % ekin)
output.write('&\n')
output.close()
temperatures = np.array(temperatures)
mean = sum(temperatures) / len(temperatures)
print 'Mean temperature:', mean, 'eV'
print
print 'This test is statistical, and may in rare cases fail due to a'
print 'statistical fluctuation.'
print
assert abs(mean - temp) <= reltol*temp, 'Deviation is too large.'
print 'Mean temperature:', mean, ' in ', temp, ' +/- ', reltol*temp
return fitdata, params, temperatures
def learn_pes_by_anealing(atoms,
gp,
cutoff,
calculator=None,
model=None,
dt=2.,
ediff=0.01,
volatile=None,
target_temperature=1000.,
stages=1,
equilibration=5,
rescale_velocities=1.05,
algorithm='fastfast',
name='model',
overwrite=True,
traj='anealing.traj',
logfile='leapfrog.log'):
assert rescale_velocities > 1
if model is not None:
if type(model) == str:
model = PosteriorPotentialFromFolder(model)
if gp is None:
gp = model.gp
if atoms.get_velocities() is None:
t = target_temperature / stages
MaxwellBoltzmannDistribution(atoms, t * units.kB)
Stationary(atoms)
ZeroRotation(atoms)
dyn = VelocityVerlet(atoms, dt * units.fs, trajectory=traj)
dyn = Leapfrog(dyn,
gp,
cutoff,
calculator=calculator,
model=model,
ediff=ediff,
volatile=volatile,
algorithm=algorithm,
logfile=logfile)
# initial equilibration
while dyn.volatile():
_, e, t, s = dyn.run_updates(1)
_, e, t, s = dyn.run_updates(equilibration)
temperatures = np.linspace(t, target_temperature, stages + 1)[1:]
heating = t < target_temperature
cooling = not heating
for k, target_t in enumerate(temperatures):
print(
'stage: {}, temperature: {}, target temperature: {}, ({})'.format(
k, t, target_t, 'heating' if heating else 'cooling'))
while (heating and t < target_t) or (cooling and t > target_t):
dyn.rescale_velocities(rescale_velocities if heating else 1. /
rescale_velocities)
_, e, t, s = dyn.run_updates(equilibration)
if k == stages - 1:
dyn.model.to_folder(name,
info='temperature: {}'.format(t),
overwrite=overwrite)
else:
dyn.model.to_folder('{}_{}'.format(name, k),
info='temperature: {}'.format(t),
overwrite=overwrite)
return dyn.get_atoms(), dyn.model
(abs(atoms.positions[:, 1] - bottom) < 1.0))
fix_atoms = FixAtoms(mask=fixed_mask)
strain_atoms = ConstantStrainRate(orig_height, strain_rate*timestep)
atoms.set_constraint([fix_atoms, strain_atoms])
mm_pot = Potential("IP SW", cutoff_skin=cutoff_skin)
mm_pot.set_default_properties(['stresses'])
atoms.set_calculator(mm_pot)
# ********* Setup and run MD ***********
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
dynamics = VelocityVerlet(atoms, timestep)
def printstatus():
if dynamics.nsteps == 1:
print """
State Time/fs Temp/K Strain G/(J/m^2) CrackPos/A D(CrackPos)/A
---------------------------------------------------------------------------------"""
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)
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)
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)
print 'No cell geometry given, specifiy either disloc or crack', 1/0
# ********* Setup and run MD ***********
# Set the initial temperature to 2*simT: it will then equilibriate to
# simT, by the virial theorem
if params.test_mode:
np.random.seed(0) # use same random seed each time to be deterministic
if params.rescale_velo:
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
# Save frames to the trajectory every `traj_interval` time steps
# but only when interpolating
trajectory = AtomsWriter(os.path.join(params.rundir, params.traj_file))
# Initialise the dynamical system
system_timer('init_dynamics')
if params.extrapolate_steps == 1:
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)