[gpaw-users] external potential for Langevin molecular dynamics

[Francisco Cano Marchal]

Solved, thank you.

Francisco Cano Marchal

El dom., 12 ago. 2018 a las 17:54, Ask Hjorth Larsen (<asklarsen at gmail.com>)
escribió:

> Hi,
>
> 2018-08-11 10:44 GMT-05:00 Francisco Cano Marchal via gpaw-users
> <gpaw-users at listserv.fysik.dtu.dk>:
> > Dear GPAW users
> >
> > I am trying to run a Langevin molecular dynamics simulation of a water
> dimer
> > in a confining potential, which I define using the 'ExternalPotential'
> class
> > and include in the calculator through the 'external' parameter. I can
> > calculate the energy of the system. When I try to run the Langevin
> dynamics
> > I get the following error. I am using Anaconda 1.7.0 on Mac OS X 10.10.5
> and
> > Python 2.7.
> >
> > TypeError: <__main__.WellTubePotential instance at 0x1166fa710> is not
> JSON
> > serializable
> >
> > I would like to know if the 'external' parameter for the GPAW calculator
> can
> > be used with Langevin dynamics or if you can give me a hint on where the
> > problem could be. I enclose my code.
> >
> > Kind regards,
> >
> > Francisco
> >
> > from ase.units import Bohr
> > from gpaw import GPAW, PW
> > from gpaw.external import ExternalPotential
> > from ase.data import s22
> > from ase.md import Langevin
> > from ase.io.trajectory import Trajectory
> > import ase.units as units
> >
> >
> > a = 4.0
> >
> > atoms = s22.create_s22_system('Water_dimer')
> > atoms.set_cell((2*a,a,a))
> > atoms.center()
> >
> > d = 4 # diameter of the tube
> > h = 200 # well depth
> >
> > class WellTubePotential(ExternalPotential):
> >     def calculate_potential(self, gd):
> >         r_vg = gd.get_grid_point_coordinates()
> >         self.vext_g = (((r_vg[1] - a / Bohr / 2)**2 + (r_vg[2] - a /
> Bohr /
> > 2)**2)**.5 > d/2)*h
>
> Implement a todict() method:
>
> def todict(self):
>   return {...}
>
> This makes it possible to save a representation of the class in the
> traj file.  You choose what to put in the dictionary.
>
> Best regards
> Ask
>
>
> >
> > calc = GPAW(external=WellTubePotential(), mode=PW(200))
> >
> > atoms.calc = calc
> > atoms.get_potential_energy()
> >
> > # Langevin Dynamics
> >
> > tag = 'dimer-in-tubewell'
> >
> > md = Langevin(atoms, 1 * units.fs, temperature=300 * units.kB,
> >               friction=0.01, logfile=tag + '.log')
> >
> > traj = Trajectory(tag + '.traj', 'w', atoms)
> > md.attach(traj.write, interval=1)
> > md.run(4000)
> >
> >
> > _______________________________________________
> > gpaw-users mailing list
> > gpaw-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
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