Chimie Théorique » QMX

#/usr/bin/env python

#PBS -l nodes=4:ppn=8

#PBS -l walltime=02:15:00

from ase import Atom, Atoms

from ase.io import read

from ase.constraints import FixAtoms

from ase.optimize.test import run_test

from gpaw import GPAW

from gpaw import Mixer

from gpaw.poisson import PoissonSolver

name = 'nanoparticle'

def get_atoms():

    atoms = Atoms([

        Atom('Pd', [5.078689759346383, 5.410678028467162, 4.000000000000000]),

        Atom('Pd', [7.522055777772603, 4.000000000000000, 4.000000000000000]),

        Atom('Pd', [7.522055777772603, 6.821356056934325, 4.000000000000000]),

        Atom('Pd', [6.707600438297196, 5.410678028467162, 6.303627574066606]),

        Atom('N',  [4.807604264052752, 5.728625577716107, 5.919407072553396]),

        Atom('H',  [4.000000000000000, 5.965167390141987, 6.490469524180266]),

    ])

    constraint = FixAtoms(mask=[a.symbol == 'Pd' for a in atoms])

    atoms.set_constraint(constraint)

    atoms.center(vacuum=4.0)

    atoms.set_pbc(False)

    return atoms

def get_calculator():

    calc = GPAW(gpts=(64, 64, 64), #h=0.18, gives 64x60x60

                mode='lcao',

                basis='szp(dzp)',

                nbands=-5,

                xc='LDA',

                width=0.1,

                mixer=Mixer(beta=0.1, nmaxold=5, weight=50.0),

                poissonsolver=PoissonSolver(nn='M', relax='GS'),

                convergence={'energy': 1e-4, 'bands': -3},

                stencils=(3, 3),

                txt='nanoparticle.txt')

    return calc

run_test(get_atoms, get_calculator, name, fmax=0.05, steps=200)