Chimie Théorique » QMX

from ase import Atoms, Atom

from ase.calculators.emt import EMT

from ase.constraints import FixAtoms

from ase.optimize.test import run_test

name = 'N2Cu'

def get_atoms_surf():

    a = 2.70

    c = 1.59 * a

    h = 1.85

    d = 1.10

    slab = Atoms('2Cu', [(0., 0., 0.), (1/3., 1/3., -0.5*c)], 

                 tags=(0, 1),

                 pbc=(1, 1, 0))

    slab.set_cell([(a, 0, 0),

                   (a / 2, 3**0.5 * a / 2, 0),

                   (0, 0, 1)])

    slab = slab.repeat((4, 4, 1))

    mask = [a.tag == 1 for a in slab]

    slab.set_constraint(FixAtoms(mask=mask))

    return slab

def get_atoms_adsorbate():

    # We need the relaxed slab here! 

    slab = Atoms([

        Atom('Cu', [     -1.028468159509163,     -0.432387156877267,     -0.202086055768265]),

        Atom('Cu', [      0.333333333333333,      0.333333333333333,     -2.146500000000000]),

        Atom('Cu', [      1.671531840490805,     -0.432387156877287,     -0.202086055768242]),

        Atom('Cu', [      3.033333333333334,      0.333333333333333,     -2.146500000000000]),

        Atom('Cu', [      4.371531840490810,     -0.432387156877236,     -0.202086055768261]),

        Atom('Cu', [      5.733333333333333,      0.333333333333333,     -2.146500000000000]),

        Atom('Cu', [      7.071531840490944,     -0.432387156877258,     -0.202086055768294]),

        Atom('Cu', [      8.433333333333335,      0.333333333333333,     -2.146500000000000]),

        Atom('Cu', [      0.321531840490810,      1.905881433340708,     -0.202086055768213]),

        Atom('Cu', [      1.683333333333333,      2.671601923551318,     -2.146500000000000]),

        Atom('Cu', [      3.021531840490771,      1.905881433340728,     -0.202086055768250]),

        Atom('Cu', [      4.383333333333334,      2.671601923551318,     -2.146500000000000]),

        Atom('Cu', [      5.721531840490857,      1.905881433340735,     -0.202086055768267]),

        Atom('Cu', [      7.083333333333333,      2.671601923551318,     -2.146500000000000]),

        Atom('Cu', [      8.421531840490820,      1.905881433340739,     -0.202086055768265]),

        Atom('Cu', [      9.783333333333335,      2.671601923551318,     -2.146500000000000]),

        Atom('Cu', [      1.671531840490742,      4.244150023558601,     -0.202086055768165]),

        Atom('Cu', [      3.033333333333334,      5.009870513769302,     -2.146500000000000]),

        Atom('Cu', [      4.371531840490840,      4.244150023558694,     -0.202086055768265]),

        Atom('Cu', [      5.733333333333333,      5.009870513769302,     -2.146500000000000]),

        Atom('Cu', [      7.071531840490880,      4.244150023558786,     -0.202086055768352]),

        Atom('Cu', [      8.433333333333335,      5.009870513769302,     -2.146500000000000]),

        Atom('Cu', [      9.771531840491031,      4.244150023558828,     -0.202086055768371]),

        Atom('Cu', [     11.133333333333335,      5.009870513769302,     -2.146500000000000]),

        Atom('Cu', [      3.021531840490714,      6.582418613776583,     -0.202086055768197]),

        Atom('Cu', [      4.383333333333334,      7.348139103987287,     -2.146500000000000]),

        Atom('Cu', [      5.721531840490814,      6.582418613776629,     -0.202086055768203]),

        Atom('Cu', [      7.083333333333333,      7.348139103987287,     -2.146500000000000]),

        Atom('Cu', [      8.421531840490985,      6.582418613776876,     -0.202086055768357]),

        Atom('Cu', [      9.783333333333335,      7.348139103987287,     -2.146500000000000]),

        Atom('Cu', [     11.121531840490929,      6.582418613776676,     -0.202086055768221]),

        Atom('Cu', [     12.483333333333334,      7.348139103987287,     -2.146500000000000]),

    ])

    mask = [a.position[2] < -1 for a in slab]

    slab.set_constraint(FixAtoms(mask=mask))

    a = 2.70

    c = 1.59 * a

    h = 1.85

    d = 1.10

    x = slab.positions[0, 2] / (c / 2) * 100

    molecule = Atoms('2N', positions=[(0., 0., h),

                                      (0., 0., h + d)])

    molecule.set_calculator(EMT())

    slab.extend(molecule)

    return slab

def get_calculator():

    return EMT()

run_test(get_atoms_surf, get_calculator, name + '-surf', steps=200)

run_test(get_atoms_adsorbate, get_calculator, name + '-N2', steps=200)