Python FaceCenteredCubic.get_kinetic_energy方法代码示例

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_kinetic_energy [as 别名]
    raise

initr = atoms.get_positions()
initp = atoms.get_momenta()


def targetfunc(params, x):
    return params[0] * exp(-params[1] * x) + params[2]

output = file("Langevin.dat", "w")

for temp, frict in ((0.01, 0.001),):
    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()/natoms
    print ekin
    output.write("%.8f\n" % ekin)
    temperatures = [(0, 2.0 / 3.0 * ekin)]
    a = 0.1
    b = frict
    c = temp
    print "Equilibrating ..."
    tstart = time.time()
    for i in xrange(1,nequil+1):
        dyn.run(nminor)
        ekin = atoms.get_kinetic_energy() / natoms
        if i % nequilprint == 0:
            print "%.6f  T = %.6f (goal: %f)" % \
                  (ekin, 2./3. * ekin, temp)
        output.write("%.8f\n" % ekin)

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_kinetic_energy [as 别名]
from asap3 import Atoms, EMT, units
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet

# Create the atoms
atoms = FaceCenteredCubic(size=(3,3,3), symbol="Cu", pbc=False)

# Give the first atom a non-zero momentum
atoms[0].set_momentum(array([0, -11.3, 0]))
print "Kinetic energies of all atoms:"
p = atoms.get_momenta()
kinenergies = 0.5 * (p * p).sum(1) / atoms.get_masses()
print kinenergies

# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())

# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0*units.fs)
print ""
print "Energy per atom:"
print "  %15s %15s %15s" % ("Pot. energy", "Kin. energy", "Total energy")

for i in range(25):
    dyn.run(10)
    epot = atoms.get_potential_energy()/len(atoms)
    ekin = atoms.get_kinetic_energy()/len(atoms)
    print "%15.5f %15.5f %15.5f" % (epot, ekin, epot+ekin)

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_kinetic_energy [as 别名]
if not hasattr(NPT, '_npt_version'):
    print "Skipping test: NP dynamics does not work in parallel with this old version of ASE."
else:
    if ismaster:
        atoms = FaceCenteredCubic(size=(30,15,15), symbol="Cu", pbc=True)
    else:
        atoms = None
    atoms = MakeParallelAtoms(atoms, cpulayout)
    atoms.set_calculator(EMT())
    print "Number of atoms:", atoms.get_number_of_atoms()

    print "Heating to %d K using Langevin" % T_goal
    lgv = Langevin(atoms, 5 * units.fs, temperature=2*T_goal*units.kB, friction=0.05)

    while atoms.get_kinetic_energy() < 1.5 * atoms.get_number_of_atoms() * T_goal * units.kB:
        lgv.run(5)
        T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() * units.kB)
        print "Temperature is now %.2f K" % (T,)
    print "Desired temperature reached!"

    lgv.set_temperature(T_goal*units.kB)

    for i in range(2):
        lgv.run(20)
        s = atoms.get_stress()
        p = -(s[0] + s[1] + s[2])/3.0 / units.GPa
        T = atoms.get_kinetic_energy() / (1.5 * atoms.get_number_of_atoms() * units.kB)
        print "Pressure is %f GPa, desired pressure is %f GPa (T = %.2f K)" % (p, p_goal, T)
        dv = (p - p_goal) / bulk
        print "Adjusting volume by", dv

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_kinetic_energy [as 别名]
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.lattice.cubic import FaceCenteredCubic

atoms = FaceCenteredCubic(size=(50,50,50), symbol="Cu", pbc=False)
print "Number of atoms:", len(atoms)
MaxwellBoltzmannDistribution(atoms, 0.1)
temp = atoms.get_kinetic_energy() / (1.5 * len(atoms))

print "Temperature", temp, " (should be 0.1)"
assert abs(temp - 0.1) < 1e-3

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_kinetic_energy [as 别名]
 atoms.set_calculator(EMT())
 MaxwellBoltzmannDistribution(atoms, 3000*units.kB)
 if ismaster:
     print "Initializing"
 e_st_pot = atoms.get_potential_energy()/natoms
 try:
     e_start_pot = e_start_dict[boundary]
 except KeyError:
     e_start_pot = e_start_dict[boundary] = e_st_pot
 else:
      ReportTest("Initial energy ", e_st_pot, e_start_pot, 1e-4,
                 silent=True)
 dyn = VelocityVerlet(atoms, logfile="-", dt=3*units.fs, loginterval=1)
 dyn.run(50)
 e_start = (atoms.get_potential_energy() 
            + atoms.get_kinetic_energy())/natoms
 if ismaster:
     print "Running"
 dyn = VelocityVerlet(atoms, dt=5*units.fs)
 logger = MDLogger(dyn, atoms, '-', peratom=True)
 logger()
 dyn.attach(logger, interval=25)
 if writetraj:
     if cpulayout is None:
         tname = "longVerlet-serial-%d-%d-%d.traj" % tuple(boundary)
     else:
         tname = ("longVerlet-%d-%d-%d--%d-%d-%d.traj" %
                  (tuple(cpulayout) + tuple(boundary)))
     traj = PickleTrajectory(tname, "w", atoms)
     traj.write()
     dyn.attach(traj, interval=1000)

# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import get_kinetic_energy [as 别名]
else:
    raise RuntimeError, "Expected zero or two parameter to the script!"

#ReportTest.Verbose()

atoms = FaceCenteredCubic(directions=((1,0,0), (0,1,0), (0,0,1)),
                          size=(15,15,15), symbol="Cu", pbc=True)
atoms.set_calculator(EMT())
print "Number of atoms:", len(atoms)

print "Heating to %d K using Langevin" % T_goal
lgv = Langevin(atoms, 5 * units.fs, temperature=2*T_goal*units.kB,
               friction=0.01)
MaxwellBoltzmannDistribution(atoms, 0.9*T_goal*units.kB)

while atoms.get_kinetic_energy() < 1.5 * len(atoms) * T_goal * units.kB:
    lgv.run(10)
    T = atoms.get_kinetic_energy() / (1.5 * len(atoms) * units.kB)
    print "Temperature is now %.2f K" % (T,)
print "Desired temperature reached!"

lgv.set_temperature(T_goal*units.kB)

for i in range(4):
    lgv.run(100)
    s = atoms.get_stress()
    p = -(s[0] + s[1] + s[2])/3.0 / units.GPa
    T = atoms.get_kinetic_energy() / (1.5 * len(atoms) * units.kB)
    print "Pressure is %f GPa, desired pressure is %f GPa (T = %.2f K)" % (p, p_goal, T)
    dv = (p - p_goal) / bulk
    print "Adjusting volume by", dv