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()
with VelocityVerlet(atoms, 0.5 * units.fs) as dyn:
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert abs(energy_start - energy_end) < 1e-4
def __init__(self, atoms: Atoms, oszicar: Oszicar, name: str=None, time: float=None):
if name is None:
self.name = str(self.atoms)
else:
self.name = name
self.time = time
self.atoms = atoms
self.potential_energy = atoms.get_potential_energy()
self.kinetic_energy = atoms.get_kinetic_energy()
self.total_energy = atoms.get_total_energy()
self.temperature = atoms.get_temperature()
# self.magmom = atoms.get_magnetic_moment()
self.elements = Counter(atoms.get_chemical_symbols())
self.set_area()
self.set_oszicar(oszicar)
n = len(atoms)
if self.get('F'):
self.F_n = self.F / n
else:
self.F_n = self.potential_energy / n
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 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 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"')
