[ase-users] Question about Constant temperature MD to melt the nanotube

[Hind Almisbahi]

Dear All

I am new to ASE. I went through the tutorials and I am trying to make the
same as the example of  melting a chunck of copper as in this link (
https://wiki.fysik.dtu.dk/ase/tutorials/md/md.html) under the constant
temperature MD. I am trying to see the melting point of the nanotube so I
wrote the following script:

***************************
from ase.structure import nanotube
from ase.calculators.emt import EMT
from ase.md.langevin import Langevin
from ase.io.trajectory import PickleTrajectory
from ase import units

T = 1500 # Kelvin
atoms = nanotube(6, 0, length=10)
atoms.set_calculator(EMT())

dyn = Langevin(atoms, 2*units.fs, T*units.kB, 0.002)
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=50)

traj = PickleTrajectory("moldyn.traj", 'w', atoms)
dyn.attach(traj.write, interval=50)

# Now run the dynamics
printenergy()
dyn.run(5000)
**************************************
However, I got bad results and the atoms are blowing up.
Hence I Tryied to use NVTBerendsen instead of Langevin and I declare its
object as following
dyn = NVTBerendsen(atoms, 0.5 * units.fs, T, taut=0.5*1000*units.fs)
As you can see I decreased the time step. Also I run this simulation to
200000 steps instead of 5000.
However the result also not good although now the atoms are not blowing up.
The diameter of the nanotube is getting wider and then smaller frequently.
I thought that the diameter should only increase gradually. Aslo even
when the temperature reached to 5000K the bonds does not start to break but
they are stretching highly. One of the strange things in the output is that
all the parts of the nanotube have exactly the same shape, while I thought
from the output of the published simulation studies that some of the
hexagon get wider while other are smaller.
Would you please help me to to know what I am missing.
I tryied also the Hotbit calculator but unfortunately with similar results.

-- 
Best Regards,
Hind Almisbahi
PhD student
Computing department
Faculty of Engineering and Physics Science
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